A good way of making sure that Blacks remain oppressed and make it even easier for secession to succeed and be further divided into little fiefdoms.
Nonsense! Regarding your impression secession would be easier than ever, the communities are individually far too small to be viable nation-states. I mentioned provision for them to form compacts which can de facto unify a coherent government across substantial populations and areas, but everything the communities do is fundamentally subject to Federal regulation. Secession could theoretically happen, if the Federal government were to be captured by a faction hell bent on it, but a faction capable of controlling Congress and the Presidency would be in a position to just run the whole unified country in its interests anyway--why then secede?
I think you are simply assuming that sociological and political facts on the ground OTL must automatically carry over in a different constitutional frame, which generally is a fair heuristic, but this seems also to be applied very selectively--it seems you assume the Reconstruction Amendments don't get made whereas I assume that such provisions as birthright citizenship, the norm of full franchise for all adult males (later to have the threshold age lowered and women also included) regardless of "race, color, creed or previous condition of servitude," and the affirmation of a Federal duty to uphold equal protection under the law, will appear not as amendments but in the main body of the new Constitution itself. But on the contrary you also assume the party line of the Redeemers and subsequent incarnations of Southern and national white supremacy must automatically carry over with the same force and predominance as OTL. But OTL, African American political representation was dependent on their maintaining equal access within state systems, and white supremacists were able to leverage the state machinery of even states with such high AA populations as South Carolina or Louisiana to shut them out of representation on both state and Federal levels, and then move, given the tacit assent of non-Southern regional political blocs to stand back from interfering, and much reinforced by the concept that the states were co-sovereign with the Union and the Federal government needed special justifications to intervene, to systematically impose second class citizenship on its "nonwhite" citizens thus making them subjects.
Here on the other hand, only the Federal government has sovereignty; no community government is immune by default to Federal oversight. That can indeed cut both ways of course and a strongly racist national consensus could have a decimating effect via Congressional fiats on the viability of minority representation and effective self defense--however I detail considerations below why I think that would be unlikely to happen.
To begin with, the specific context of the introduction of this system to the South is the Union dismantling, in the wake of a constitutional convention in 1864, Southern and Northern states alike, and the definition and organization per the new Constitution of the communities. The Union Army will have control on the ground of territory it subdues, and will have found African Americans freed under the Emancipation Proclamation useful auxiliaries, as well as later in the war accepting them as volunteer troops. So they will not fail to establish appropriately coherent African American communities and get them up to speed in constitutional terms, their adult male populations voting both for their local self-government and for representation in Congress by 1866--indeed in the circumstances, it is possible that Representatives will be elected and admitted ad hoc as soon as complexes of communities of sufficient population are organized.
There would then be no state governments, north or south, to do such things as disfranchise African Americans en masse, or devise Black Codes to criminalize them with Catch-22s and thus de facto reenslave them under the rubric of punishment for felonies. The law is Federal law and those adopted by the autonomous communities, including any multilateral compacts among them.
Note that the community territories will not necessarily fill the map of the USA; geographic reach of a community will be determined by the actual economic activities centered on it and regions into which no community systematically reaches in regular operations will revert to Federal territory.
Now of course white-majority communities will be pretty numerous and grasping of territory overall, but their own regulations will only apply to their domains, and someone resident in another community will always have grounds for appealing to federal courts and other extra-community agencies for intervention.
OTL Klan terrorism could strike a black settlement or house and any attempt at recourse via the justice system would have to be made in a courtroom of the state ostensibly including both parties as citizens, but objectively under the control of the same side that committed the offense.
Here many, perhaps most, African American citizens will reside on community territory that is in the jurisdiction of their own people, and the protocols of justice will tend to remand the case to a courtroom in the offended party's jurisdiction. Disputes that involve both white supremacist and African communities would be generally settled in Federal courts. Possibly Congress would permit the formation of regional compact associations that might be permitted benches of their own, as something agreed to and cooperatively maintained by all involved communities, and all this under Federal oversight and potential intervention.
Broadly speaking, the balance of power would enable African American communities to maintain quite a vigorous self defense as a final layer of self protection. Aside from a right, indeed mandate, for each to provide police services, they will have their militias, connected with contingency plans to the Union military command. If African American majority communities come under attack systematically, they have these lines of defense. I presume it will be encoded in law as a matter of course that actual violence of any kind involving community officers beyond normal police work will require some Congressionally overseen review of the events, and endemic ongoing violence demand Federal intervention. So while that is not the same thing as total immunity to systematic terrorism fostered in the white supremacist communities, it is a defense enabling AA communities to withstand it and seek orderly redress in the Federal system, or by coming to agreements locally that effectively suppress this. If the level of terrorism that must be endured is not sufficient to shut down the AA communities, they at any rate endure. Now with new grievances of course.
I trust you are aware of many swathes of territory in the Civil War era South where AA populations predominated demographically, including being a majority in the state of South Carolina, as well as the "Black Belt" across Mississippi, Alabama and I believe reaching into Georgia, and I have recently learned in large sections of Tidewater Virginia. Each of these zones would, despite being salted as it were with white-majority communities, be strongholds of AA autonomy. In the event that US society veers hard into pervasive racism as the norm, it would be possible for AA strongholds, which might also come to include important sections of developing cities, and perhaps zones elsewhere in the Union, to close ranks and react to white apartheid with black self-reliance. I hope separatism would not be the general solution to US racial relations, but it is a viable option and being a potential response, tends to deter support for white supremacist extremism.
Beyond that, the inalienable ability of at least some African American communities to elect members of Congress on their own would promote alliances between African American representatives and "white" ones. It would be quite likely therefore that by the time a decade had elapsed since the surrender of the remaining Confederate authority, quite a lot of politicians at the national level would recognize obligations to these communities, and indeed I think that while considerable strength would remain with the white supremacist position, African Americans would retain allies locally in the South they could not sustain OTL.
Indeed parallel to their position in Congress, and thus probably able to entrench themselves more or less proportionally in federal Executive employment as well, we can expect that the dynamic of racist separatism would tend to penalize bastions of white supremacy. Little would stop AA minorities in such community zones, if they judge themselves underappreciated and ill treated, from voting with their feet and moving--and a ready answer to anyone who bemoans the plight of white people "trapped" in AA majority communities will be that if they can't really abide it they too can leave. Although any dominant class tends to discount and disparage the degree to which general prosperity depends on their underclasses, the fact is much Southern economic potential comes from the employment of "black" labor, and if the citizens in question are motivated to up stakes and move to a reasonably nearby (or distant) AA bastion, or just someplace with white majorities who are more reasonable, they will suffer a serious labor drain, while communities and regions where more tolerant, accepting, even perhaps not too long after embracing attitudes to AA citizens develop instead, will be more prosperous and tend to set the tone for regional norms across the board. This is my major hope of course, that gradually the South will move toward racial inclusion. It is not necessary this happens everywhere for it to take root as an alternative narrative to the stories white supremacists tell, giving them the lie.
The more bailiwicks there are in which African Americans, and other disparaged minorities, are masters in their own house, the more a general penumbra of protection in consideration of overall national balance of power there is even to isolated minority communities in a region of "white" dominated communities, and even to individuals resident in such communities.
Therefore I doubt very much that such a United State of America would mirror the trajectory of Jim Crow too closely. It might be exactly as bad as OTL in some bailiwicks, but the general cover for extremism on these fronts given by Redeemers and their successors being able to seize control of state machinery and impose their order wholesale on entire regions would be quite badly eroded, tipping the balance of skepticism against OTL allies who, if only by neutral default, permitted them to have their reign of terror unchecked. National institutions might indeed be more biased against African Americans and other minorities than they ought to be, but every minority community will manage to have certain bastions in which they set the norms, and these I predict will in turn foster tolerant mixed communities and cosmopolitan ones. Extremist white supremacist communities would, far from establishing themselves as the benchmark of normal national policy as OTL, tend to be isolated and marginal in influence, and under considerable pressure to reconsider their positions.
OTL Jim Crow among many other things impeded travel for African Americans and other discriminated against minorities, and I believe this remains a problem today. It will be an obvious necessity, which a Republican dominated Federal regime that has just fought and won the Civil War will recognize and provide for, to guarantee rights of transit, to give at least limited protection to travelers who don't intrude too deeply into even quite hostile communities on the way. Again the ultimate judges of this will be Federal officials, the Federal courts and Congress as arbiter of community charters and compacts.
The Federal judiciary will have to be much expanded; to some extent the work formerly done by state court systems will be taken up by community courts, but the balance that is not will have to be folded over to the Federal system. I suppose the number of Federal Circuits would be much increased, and the suddenly unemployed state justices will be recruited and approved en masse to fill the new Federal benches. At least, in the particular proposed TL, this happens in the North and West, but the South in rebellion will have discredited their former state judges by their collusion with secessionism, and the invading and occupying Union forces will have something to say about who the newly imposed Federal authority will appoint to fill the corresponding Southern circuit seats. We can be sure that once seated, these judges will tend to remain until they are promoted or retire, and this buys a long period of time for Southern communities to reach some kind of new equilibrium, in which time, community courts, which will become the major source of replacement judges across the nation, can mature and provide candidates with good credentials to be placed in these seats. Congress might choose to devolve some say by the communities affected in who these appointees are, and they would generally derive from the regions they preside over, so a distinctly Southern self-rule has several regional bases--their regional control of their regional courts, the proposed Senate system I offered where the USA is divided into sixteen districts to elect one Senator per class and indirectly probably elect a second one from the region; I'd have to look at the Census numbers but off the top of my head the South will comprise between three and six of these 16 zones--the borders will fluctuate from census to census as demographics shift, but broadly speaking the southeast must hold at least a quarter if not more of the US population. The more regional devolution of their basic authority Congress deems pragmatic the more local control there is in the form of compacts associating communities on a mutually agreeable basis.
It is not sustainable to hold the South in special subjugation over the long term, but neither is it necessary to assume Southern culture must replicate every obnoxious feature and be dominated by every stereotype that holds OTL. I think in your dismissive response this is what you must be assuming.
As a general thing, by the way, I disagree with the conventional wisdom that the more local the government, the more democratic and inclusive of its subjects it tends to be. Here in the USA OTL, it is rather the reverse, with citizens generally paying more attention to the highest levels, especially the President, and so on down the ladder, while local government often flies under the radar of most citizen attention. I believe Rosa Luxemburg had similar contrarian arguments based on sound reasoning and observation in her polemics about policy in the German Social Democratic Party, arguing for more democracy in strong central government rather than devolution of control to more local powers. I therefore did not offer this as a general panacea I believe in (that would apply more to my remarks about proportional representation in legislatures). But given my knowledge about how Reconstruction went and how reaction rolled it back, I do think that the power of the states was pretty critical. And in the context of an overarching strong central government, which I have provided for here, I do think there is a general principle that the more finely chopped up the regional level in a federal system is, the more unified the resulting polity can be as a whole, and the more opportunity there is for resolving regional conflicts. Thus, a USA of tens or hundreds of thousands of small communities, especially in the context of a strong and democratic central government and a strong commitment to inclusive democracy, would seem superior to me to the current state system. So while it is the specific OP question that moved me to flesh it out conceptually, it is also indeed something I think would be worth considering arising in any era.
Having once again mentioned PR, I suggest also that if it seems precocious in the mid-19th century, perhaps it should not be too strange Americans might take pride in an advanced innovation. More to the point, observing that robust proportional representation offers a pretty automatic counterweight against any ill effects arising from unequal districting, I thought it might be catalyzed by a desire to provide for Congressional representation by forming districts out of communities as units, which would tend to limit the ability to form districts of equal size even for one snapshot in time. But with the total delegation of Congress and perhaps a Senate derived from consideration of the total national vote integrated, overrepresentation by district seats for some underpopulated districts and overpopulation diluting that plurality seat FPTP representation in others, is automatically compensated especially if we make up the balanced party delegations by choosing candidates who ran in districts for these seats too, based on the number of votes they received. Note that it also has the effect of automatically penalizing districts dominated by communities that might choose to repress votes; the more success they have at barring specific targeted groups from voting, the smaller their total delegation becomes, in favor of other regions with higher turnout.
I strongly disbelieve a USA that evolved in this way could manage to have the sorts of failures of democracy OTL's Jim Crow era featured, but insofar as this does happen, the South would wind up with fewer representatives, and this would be true of the Senate system I proposed too, and of course a national popular vote for President would also feature automatically diminishing the weight of regions where voter suppression prevails--or having lower turnout for any reason. OTL I have looked at figures for Senate and House elections in the later Jim Crow era, such elections as 1948 and 1950, and the discrepancy in turnout between some Jim Crow states versus high turnout states in the Northeast and Midwest is appallingly high, approaching a factor of ten. If indeed somehow the Redeemers manage their OTL tyranny, they will pay a huge price for it in national representation! Having discarded the whole concept of the states, there would be no justification for maintaining power in Congress based on full population, when that population is partially disfranchised, and largely depressed in turnout because of the lack of competitiveness in elections. (In a spirit of bipartiansan fairness regarding a fact that dismays me, I note that California in modern elections is notably lower in turnout than the national average; as someone who thinks of himself as a "Californian in exile" this is pretty mortifying! There too, various layers relating in part to single party dominance tend to depress turnout...not that I think the California Republican's wounds were anything but self-inflicted to be sure. But having shot themselves down, the Democratic party hegemony resulting does seem rather bad for democracy as such--my preferred remedy being empowering third parties rather than making special concessions to the rival duopoly party!)