Having separate channels is how animations are defined in .glb file, that’s why it’s how it is working in Babylon. However, I don’t think it is different when the animation is coming from a .babylon file(?) The difference is that in gltf we animate transform nodes (bones are linked to transform nodes) and in .babylon file we directly animate the bones, but in the end it’s the same thing, we update a property (rotation, position, scaling) and the matrix of the transform node/bone will be recomputed from there.
Regarding sharing skeletons, GLTF Skeletons And Transform Nodes - #5 by bghgary may help, as well as Sharing skeletons between two skinned mesh · Issue #1285 · KhronosGroup/glTF · GitHub.