That is a pretty arbitrary qualifier for 3D. Doom is filled with spatial obstacles that make use of the 3D geometry. For example, a missile can pass over the player. Facing a wall on top of which a monster stands, I can't necessarily pass it or see or fire at the monster. Flattening the levels would change the game and remove many of its challenges.

The format of the levels or the fact that there are no rooms over other rooms don't really factor into it.