Room over room (as done in later build games) usually does not require the sectors to overlap in this manner as it is a different thing (it is extension of how swimable water works, where the engine renders the other sector instead of floor/ceiling).

While Lunatic Fringe is pretty in-your-face example of impossible geometry in build, the duke3d maps contain many more cases of intersecting geometry. Obviously such things are impossible in Doom because there is no way to build BSP tree out of that and because doom only tracks X/Y coordinates of player(s)/monsters.