ThreeCSG does change the geometry, by which I mean geometry in the sense of Three.js -- the collection of vertices, the faces, etc. I think what you mean is that ThreeCSG does not change the physics-based properties of your object.
According to https://github.com/chandlerprall/Physijs/wiki/Basic-Shapes , it appears as though you have to use Physijs.ConcaveMesh
as it "matches any concave geometry you have, i.e. arbitrary mesh", and it is the only one that has a change of supporting a non-convex physical object.