I remember reading that for Galaxy 2 the programming team developed an interface for all staff members to submit level designs, even the music composers and visual artists. It's brilliant, since you get so many different kinds of minds contributing ideas that someone designated to be on the level design team would've never thought up. Given how 3D is even MORE modular, I wouldn't be surprised if they had continued with that approach.
Also, I just thought about how since the level "thumbnails" float above the world they're inside (and not just modeled onto the world itself) that this probably allowed them to switch around where levels appear in the game very late in development without having to worry about remodeling the overworld map.