In the movie theatre there is a projector room up high, and the theatre exit below BUT the theatre exit has a wall centered in the middle where the overlap would be. There is also a spiral staircase going up to the projector room which has 2 or 3 levels of overlap, but as it is enclosed you don't view 2 levels at the same time.
Interesting stuff - and like many others have commented, I remember playing around with the Build editor and learning about these random hacks.
EDIT: and just now I'm remembering that submerging in water was another hack - you would actually teleport to another room on the map. In Duke3d the water was opaque, but in the later Shadow Warrior i remember it having some transparency (I assume probably using similar mirror hacks as D3d)