This is what used to happen, but it has problems that you reported. 
glTF skins are modeled from Unity which gets the bone transforms, etc. from nodes in the hierarchy. As seen in the issue you posted (HTML5 Game Devs Forum - HTML5GameDevs.com), if the runtime doesn’t match exactly with what is expected from glTF, unexpected things might happen.
When the glTF issue Sharing skeletons between two skinned mesh · Issue #1285 · KhronosGroup/glTF · GitHub gets fixed in future versions, this will be much less of an issue, but I can’t think of a good way to fix this with glTF 2.0 and Babylon.