This is an excellent point, but one of the biggest cliches of Confederate victory timelines is that Union peace negotiators are inept idiots. How often does the Union give back every bit of territory they have captured from the Confederates, plus Missouri or Kentucky as a special bonus prize in return for getting absolutely nothing from the Confederates.
I'll bite on this one. Simply calling for a plebiscite for the sake of one would be a bit ludicrous. Certainly there are timelines where the Confederacy does get Kentucky, but it's usually because either A) Kentucky seceded outright or B) the Confederate invasion in 1862 put the rival Kentucky government in power some way due to some 1862 POD. I once saw a timeline where the CSA managed to get Missouri, but not Kentucky. Much of it does depend on the particular conditions of the time. Outright demanding a plebiscite in the border states is a bit ludicrous on its face, but one could also understand why the CSA might want them in Kentucky and Missouri.
1) Control of Kentucky gives the CSA a more secure border at the Ohio River.
2) Control of Missouri gives the CSA more security for the Mississippi River.
Of course, the USA recognizes these same benefits to the CSA, so this isn't exactly something that could happen easily. Much of this depends on when the CSA wins the war. Once the rival Confederate governments of Kentucky and Missouri exist, the CSA has grounds to ask for a plebiscite. There is one situation where the demand might have success. The CSA already has troops occupying Missouri and Kentucky. At this point, the CSA might have triggered the secession of these states anyway. This is entirely possible in a Trent War timeline. The USA wouldn't exactly be negotiating from a position of strength here. Of course, this outlines all sorts of possible worst case scenarios depending on the success of various Confederate campaigns. General ineptness would likely create far too many difficulties in the Trans-Mississippi for the CSA, but higher rates of success in the West (Tennessee and Kentucky) and the East (Virginia and Maryland) don't seem completely implausible in a Trent War timeline.
As to post war borders, the Union wouldn't give up anything more than the original seceding states, and might (I stress might) allow a plebiscite in Kentucky if the Confederacy relinquished its claims to Maryland, West Virginia, and Missouri, and that would only happen if Confederate troops were sitting on the soil of Kentucky when negotiations started. The only other territory they might give up is Confederate Arizona, and the Indian Territory, but again, the Confederates need to be sitting on it for that to actually happen.
I'd say it all depends on various factors. How long did the war last? How successful were Confederate campaigns in Maryland, Kentucky, or Missouri? Or West Virginia, for that matter? What is the overall effect of British intervention on the Confederate war effort if that intervention actually does occur? Does France jump on the bandwagon if Britain intervenes and send direct military assistance to try to get the CSA agree to allow a French puppet on their border? At that point, I'd say all bets are off so long as they aren't completely in the realm of ASB. If there is no foreign intervention and simply just foreign recognition, the USA can still negotiate from a higher position of strength than if Britain and France actually get involved militarily.
So how do I feel about worst case scenario in the event of British and French intervention?
1) Confederate Arizona would get support from France simply because it would further reduce the Union border with Mexico, but Britain wouldn't exactly want the Confederates to take the entire American Southwest. The CSA wouldn't have any real claim to the remaining part of New Mexico Territory, so the division likely would stand.
2) Indian Territory without much question would go to the CSA. It would give the Union a more favorable border if they kept Indian Territory, but they might not war to keep it.
3) If Kentucky, Maryland, and Missouri secede during this particular war, it would be hard to argue against them. However, a lack of secession by any of these states might still be grounds for the CSA to demand a plebiscite of some sort if Confederate troops are actually present in significant numbers in those states. Britain might be far more supportive of this demand simply because it would potentially put the Confederate border closer to the Great Lakes, which would give some more security in that region. However, Britain might not support the plebiscites on anti-slavery grounds. I'd say a plebiscite for Kentucky or Missouri would be a toss up for British support. French support could also go either way, but I see the French giving much stronger backing towards Confederate claims on Arizona Territory. All of that is a big if, but we're also discussing the worst case scenario.
4) West Virginia could still remain Confederate. This is admittedly incredibly difficult to pull off and it would depend on how long the war actually drags on. Even in a worst case scenario, I'd see this having a small chance of actually happening. The CSA has a strong claim, but unless it can reverse its fortunes in West Virginia, the CSA probably won't get its way there.
Beyond that, I'd say this is the best the CSA could actually get in the worst case scenario outlined above. The CSA (with some assistance from Britain and France) actually needs to be negotiating from a better position of strength to get these sort of benefits. And even then, we're speaking of a worst case scenario for the Union. If the Union avoids the worst case scenario, but still loses the war, then it will have more strength at the negotiating table. But in no way would I ever expect "plebiscite just because."
In this same worst case scenario, Britain might be a bit vindictive and clarify ownership of the San Juan Islands, which hadn't been decided yet anyway. If Britain decides to revise the Webster-Ashburton Treaty in its favor, then a future war between the Union and Britain becomes highly likely. Everything said here would require specific conditions to give an outcome with these particular results. This also avoids completely implausible outcomes. I find it far more likely for the USA to simply bow out in 1863 and seek peace, which would avoid the worst case scenario entirely. In other words, what happens next is entirely timeline dependent.