Let say I wanted to make a level-based game taking place inside a bunker. Would I just make the underlying level geometry as one 3d model including all walls, ceilings and floors, or would I divide it into models for each room, or even for each surface?
Depends on the game engine, and the game. But it’s usually not one big thing. Also keep in mind a lot of how a game engine imports the data could be doing quite a bit behind the scene. So, refer to the engine docs or communities.