This must be a right-handed system issue, as you have already noticed. CSG is using the vertex data, which is unmodified by the parent root node transformation. Probably should be taken into account
To avoid this issue, you can bake the current transformation to the root node of the glTF loaded - Babylon.js Playground (babylonjs.com) (notice line 21). That’s for left handed systems.
I have to admit I am not sure what happened with the right handed system, but I can only assume it has something to do with the way CSG is reading the vertex data. We can investigate that, you can submit a github issue if you wish. Please link this topic (and the playground) in the github issue
I saw that @Deltakosh added this issue to 5.0.0 milestone. Unfortunately I have to solve this problem earlier. Since I always use right handed system and my project is set up for this I can’t switch to left handed system for this. Is there any workaround or fix that I can use to make csg work as expected? Do you have an idea, @Evgeni_Popov? I noticed you were assigned to this case.