Well, the bottom has enough floor, so as long as the ladders aren't in the way stuff could spawn down there. So the room should be okay, the only question is those ladders.
Depending on the size of the boss, you'll see smaller bosses spawn at the top or in other parts, too. You'd just never see the largest possible bosses (none of which are even in yet, anyway) seed in the top area. To have the very largest kind of boss seed, you need 8 tiles wide all in a row, and then 8 tiles of space above. But smaller bosses can and will seed in smaller areas, so it really varies.
My main thing is just always making sure that there's at least one 8x8 area in the map somewhere, and there is now.