Is it just me, or does it seem like whenever you defeat an enemy in a ??? room (ones like Bandit hideouts) they just... come back (presumably from the stairs).

Am I just being stupid, or is it actually happening? Is it supposed to happen? Because enemies never respawn in main floors, so I'm not sure why they'd respawn here. It's especially annoying when trying to rescue the allies who the boss decided to execute partway through the fight.

(Slight sidenote, but I don' think boss floors should even have a ??? room, it doesn't make much sense and is annoying since allies are practicalyl guaranteed to go down there)

You're speaking about "%FACTION%'s Prison" type of location.
Enemies you meet on main floors are either recon parties or strays most of the time.
Faction prisons? They live there. And are eager to defend their home.

I believe that prisons on boss floors are a side effect of having actual locations as prisons.
Which is good! Being dragged to some limbo, with a chance to lose some valuables there irreversibly, sucked.

But them respawning borderline instantly and indefinitely makes breaking allies out a frustrating mess since allies cannot stealth for the life of them and  fighting through all of that is absurd. 

I think either a spawn cap limit, or some time before respawning makes more sense, and would be fairer gameplay wise. And if all of your bandits in a hideout are constantly dying, you'd probably give up on trying to reclaim it, at least until the people taking out all your bandits leave.

Boss floors already seem to have their own furniture and cells, couldn't allies just go there? Or have a location with zero enemy spawns specifically for the boss floors. Why is Fuuka fine with a massive bandit nest literally attached to her graveyard? Why are the bandits even willing to go there? What bandit chief thought it was a good location when it's directly attached to someone else's territory who could pretty easily forcefully evict  you at a moment's notice?

They can and they will, but that's why you get rid of the enemies first. The adventage of telling your allies to stay put is that once you cleared the area around the cell, they won't seek out farther enemies on their own.  In contrast, if they follow you, clearing one path will not suffice, because your allies will happily take detours to confront otherwise perfectly avoidable enemies on sidetracks. Ideally you clear the area around the cell or furniture BEFORE you free them. Then you just fight your way out of the jail, and your allies will be right next to you once you get back to the main level.

They shouldnt be respawning in front of you. But the main reason they respawn is because otherwise escaping after clearing the room is very easy.

However if they have names and they pop up in front of you, thats due to the wandering NPCs system. Those do not infinitely respawn, theres a finite number wandering around the map.

Just installed the game and still figuring out the mechanics. So is there a room where the character gets stripped and dominated? or u have to installed a mod for it?

My plans for the generic faction prisons is to have a limit on how many can spawn each time you are thrown in jail, resetting if you are captured again.

As you keep defeating more and more of them the waves will get stronger, so farming them will have a practical limit. This will also allow lower level prisons to potentially be a destination if captured in a higher floor, thus reducing the number of redundant prisons each floor.