What do you mean "fake 3d"? They are as 3D as any other computer generated images with linear perspective. Quake is even using a rasterizer like nearly all games today.
Grass and particle effects are secondary....
How many FPS AAA titles today use sprites for enemies and weapons?
Nothing's stopping someone from adding code to render 3D models or "portals" in the game, and in fact it has already been done, with no 3D acceleration needed.
Quake was a whole new paradigm, it was based on a true 3D engine and its maps were generated in three dimensions. You could stand under stairs, under the room above, and underneath lifts.