You’re right that the documentation doesn’t explain clearly why volume overlaps are bad. Basically, the problem is that the overlap region is undefined – should it represent the physics of material A, or of material B? You can see this clearly in the way that Geant4 optimizes the geometry, by voxelizing it: in the overlap region, should the voxel be assigned to point to volume A or volume B?
When a particle is traversing your geometry, which volume it’s assigned to will depend on it’s direction of motion – entering from one side, it’ll stay in volume A as it passes through the overlap region (and therefore “ought to” experience the physics of material A), while entering from the other side it’ll stay in volume B.