Okay, I think I identified a problem. It indeed is a mod compatibility issue, specifically combat overhaul mods.
My previous testing I realized I didn't have Damn Apocalypse's combat module active, I was testing out another combat mod at the time. which gave me a red herring.
The reason why Carnal is a no-show / dead in the placeholder cell is because her record has 0 healthpoints. If you use a mod that changes how the HP formula works that doesn't use leveled HP (Damn Apocalypse's combat module in my case), that 0 HP makes Carnal dead on game initialization, and borks the quest in general. I've tried a bunch of setstage, resurrects, recycleactors, etc. and it won't fix the quest in an existing save.
I tested this by starting a new game and using the skip quest cheat. In one save with the combat overhaul mod, carnal was dead and didn't spawn in Fallon's basement.
In a second save I manually edited Carnal's NPC record to give her a non-zero healthpoints (50 for example), did the cheat skip, and the quest was working like intended.
Seeing how Carnal's HP is insignificant gameplay-wise, giving her something trivial like a base 50 HP in her record would help a lot of users with their mod load order compatibilities
@kinggath