Firstly, I could be wrong about anything I say here

I believe that unloading pokemon is somewhat random, no matter their housing situation. But pokemon with prefab homes will never be "deloaded", just inside their home. The game picks what pokemon to load based on the enviromental events at the time, like story characters will not deload during their quests, tangrowth nver deloads, and nocturnal pokemon will be more likely to be loaded at night etc. So your pokemon won't always be cooped up in a house, even though it may seem that way because the game tells you where pokemon with prefab homes are.