In one of the post for Godot 3.0 it states that the modules can be used to replace the physics system and the rendering system. However I can't actually find any information about this.
A search through the issues on the Git for Godot shows that there is someone who is successfully replacing the default Physics system with Bullet. But I still can not figure out how to do this. I don't see any sort of options in the Project Settings for this. And there's no information on the 2.1 docs.