The skill-less peasants are new and arrive with startling regularity (once every migrant wave or so), so since it's not a new version I'm pretty sure it's a bug.
Honestly, it feels like we've tried just about everything. I've scoured my raws tons upon tons of times and seen nothing amiss, yet I get problems when I place even one tiny mod into an otherwise pristine set of raws. Even more mysterious is the fact that the mods I made in 40.19 (when I first started modding) work just fine, but the game throws a hissy fit when I try anything that I hadn't put in the game then. It seems that the very act of changing raws of any type messes up the game, even though the "old" changes are just fine. The only other possible raws I can think of are in a completely separate iteration of the game, not even near the affected raws, and you said that therefore they shouldn't cause problems. I even sent you a copy of an affected world, but you couldn't find anything wrong with it.
Have you tried taking the modded creature(s) and using them in your own raws? That's one of the only things left that I can think of, aside from sending you my entire DF folder. Or should I post my "old" modded creatures alongside my "new" modded creatures to see if there's anything significantly different, even though literally one tiny tag throws everything off?