This is a legacy option that shouldn’t be used anymore.
If you want to be in left handed at the end, then you probably shouldn’t set useRightHandedSystem on the scene. You can perform the CSG in left-handed. Just make sure you don’t remove the __root__ node which has the transform to convert from right-handed glTF data to left-handed data.
(EDIT: this isn’t quite right… see correct solution below: https://playground.babylonjs.com/#DFD9IV#11)