Great suggestion.
I'd argue you might want to check to do the same for Communists, as Soviets or other Communist countries, if they were to ever win a war, as they're quite spam happy to release random puppets everywhere possible much like Democratic AI.
They actually have a little bit of this already; the communists don't take cores/claims from faction allies. (so no Soviet Occitania if France is in the Comintern) and Fascists won't take land from an ally who has an "annex" wargoal on the land in question.
Overall, I really like the suggestion that started this thread. Not doing anything to land *controlled* by an ally seems excessive, (the Dutch can end up controlling most of Germany, depending on where D-Day lands) but respecting cores and claims of allies seems extremely sensible. No more British Occitania!
IMO, the dev team usually does a pretty good job updating peace conferences. They still have their troubles, but they get better basically every expansion. (The last update to the non-fascist peace conference AI was MtG, though.)
The main issue is the ahistorical balkanization of France. They could update the Democratic/Communist/Neutral peace conference to respect France's borders more, but the peace conference AI isn't really the issue here: France should probably automatically get all of the territory owned by Vichy. (but then you run into "what happens to Indochina, which was probably owned by Japan in the peace conference?" and some weird edge cases for if Vichy happened to have annexed new colonies after being formed)