Doom64 accomplished this by adding a silent elevator sector type, so it could have bridges that appear to be floating "over" an underpass that you could walk through but you could also cross over the top. This, of course, immediately got turned into marketing bullshit trying very hard to imply that "Doom64 was fully truly 3D, and the Doom engine could now do room-over-room."

Which it can't. These weren't bridges, they were cleverly disguised elevators.

What you eventually notice is that you can never look at one of these bridges from below and then from above, or vise-versa, without first passing through a tunnel or building that completely obscures your view of it. When your view is obstructed, you cross over a trigger somewhere that causes the elevator to, without making any sound (because elevator sounds were hard coded into original Doom), zip up to its cross-over-the-top position or its walk-under-the-bottom position. It could only ever be in one state at a time, never both.