Sorry for the long delay, but this issue is a problem in the method we decided to do with this PR.
This other forum issue is also related to this PR: Inconsistent glTF Exports Between Babylon 5 and Babylon 6 - Bugs - Babylon.js (babylonjs.com)
I am planning on rewriting a lot of the glTF serializer to address a lot of short-comings and fix all of these issues, but it will take a while to complete. Sorry for the troubles.