Hi!
I believe our problem had to do something with the “separate” nature of modules inside three/examples/jsm/. We were/are using several modules from this direcory : Sky, OBJLoader, SubdivisionModifier & PMREMCubeUVPacker + PMREMGenerator. After doing 
this our bundle size was okay again (not double) + we had no issues with the geometry.id s any more.
All other three/src modules described inside src/Three.d.ts (means not inside the three/examples/jsm folder) didn’t cause any trouble.