"Floors can't have different heights in Starfox."
*links a screenshot of a flat floor in Star Fox*
The little bumps there aren't map data. I don't think they even have colliders on them.
The point of that particular shot was to show 3D geometry that the Doom engine cannot render. For example, those "little bumps" are sloped 3D geometry. The stock Doom engine isn't capable of that.
Floor height isn't even an issue here, since all we're talking about is relative positional geometry in 3D space. Star Fox is clearly capable of that as even that screenshot shows. And such levels further show when they move into angular changes in 3D geometry of the corridors themselves.
This isn't a matter of right/wrong. It's simply a matter of what the respective rendering engines are capable of re: 3D geometry.
The Doom engine cannot render much of the 3D geometry used in Star Fox. That's just a basic fact.