That certainly makes sense; also, though, the Nazis would still have the resources to both wage war and simultaneously conduct the Holocaust in this TL, correct?
Probably, yes. The death camps really didn't take up all that many resources in the grand scheme of things (the victims were murdered on arrival, so the manpower needed as e.g. guards was quite small), and in any case the Nazi ideology would very probably place killing the Jews under their control as a higher priority than winning the war: they certainly did in OTL.
Wasn't Pope Pius XII also very eager to preserve the Catholic Church's 1933 Concordat with Germany, though?
Possibly, although it needs to be remember that this is the same guy who wrote most of
Mit Brennender Sorge. My reading of it (and there are many others) is that he viewed the alternatives to it to be worse. In a no-fall-of-France scenario the areas occupied by the Germans are likely to be Poland, Czechoslovakia, Denmark, Norway and parts of Belgium and the Netherlands - of these the vast majority of the Catholic population under German control is in Poland, and with Hungary still neutral contact between Poland and the Vatican will be much more comprehensive. Given the atrocities committed against the Church in Poland in OTL, and that this is a higher priority, my suspicion is that the Concordat will be seen to be of little residual value, and the Church would act in much more direct opposition to the Nazis. That has all sorts of interesting butterflies just by itself.
It's kind of hard to go much above 90%, though. Plus, couldn't Hitler and the Nazis get successfully overthrown in the middle of WWII by anti-Nazi German military officers in this TL?
Yes and yes. However, if you're one of the ~10% of Polish Jews who survived in OTL then it's pretty bad. And just because the Nazis might get overthrown doesn't mean the Jews would be treated any better - the record of the Wehrmacht rather than SS is pretty black in this regard (being somewhat whitewashed in OTL), and the Nazis being overthrown would in any case not necessarily lead to a peace treaty. The British and French at the time regarded the problem as being Prussian Militarism rather than Fascism: a military coup isn't going to make them think the problem has gone away, nor will they accept any terms that aren't "unconditional surrender" in all but name. Essentially that means the only thing to stop this Alt-Holocaust would be British or French tanks in Poland.
Would the Nazis actually have the time to kill 90+% of Polish Jewry in this TL, though?
Almost certainly. By a relatively early stage in the war (at least a year before the OTL extermination camps started work) they were ghettoised and being severely maltreated - the three extermination camps by themselves are enough to kill virtually the entire Jewish population of Poland in the likely timeframe for such a war (ending mid-1942ish, depending on a number of other factors).
Would both the Zionists and Jordan actually be open to this federation idea, though?
That's the wrong question. In an Alt-WW2 where France doesn't collapse then Italy is very unlikely to enter the war and Japan will either stay out or get bitchslapped by a combination of the RN and USN in double-quick time. That means after the war the opinion that counts is in London, not Amman or Jerusalem. Whether London would go for it I have no idea - they're likely to try and conform to the Balfour declaration somehow however, but exactly how I have no idea.