Hence my squashing analogy, DOOM levels don't overlap and can be drawn ("squashed flat") on a 2D surface.
But you can't actually occupy a different height for a given location. This is NOT real 3D. That's why DOOM is sometimes described as a 2.5D game. Quake was the ID Software game that was 3D.
If you think DOOM is a 3D game, try creating a level that contains a player accessible location above/below another player accessible location, and see how the game renders it. Or, read the DOOM rendering engine links that are posted and pay close attention to the "not a true 3D engine" paragraph.
The format of the levels or the fact that there are no rooms over other rooms don't really factor into it.
I suppose at the extreme end, I'd have to explain why Wizardry on the Apple II is or isn't a 3D game, which would be more of a strained philosophical argument.
You could argue there are no 3D graphics. Everything is transformed into a 2D screen representation.