A Clear isn't really a stealthy operation by nature; you'll be making your presence known to everything, so, the incompatibility doesn't really bother me. The fact that you actually can 'clear' the kitchen with a shotgun and then step over to the oblivious living room and "sneak" that part is lot weirder.
The closets themselves seem to get worse every iteration; they're annoying enough at the moment that I'd be happier if the game just honestly spawned zeds behind me instead. We've had zeds sitting on roof tiles that can't carry their weight, as evidenced by the moment they activate; they fall. Now we have zeds "wallpapered" in to structurally ridiculous shelves above staircases and "wallpapered" within brick walls. These make the world feel like one massive gimmick-fest.
I'm just waiting 'til the poi designers figure out you can flip a pressure plate mine around, paint it as carpet, and replace a floor block... hey, at least it would be more realistic.
One way to make 'clearing' more compatible would be to handle the POI sections like an actual clear operation would. Make the quest actually have you check all the corners and cupboards and ceilings, leaving no room for missed spawns. I don't like the idea, since it would become a hand-holding icon hunt instead of anything resembling a world, but it would "work" better.