As far as the code is concerned, the only difference is that both groups have to be added to animations instead of only one group. It only becomes a problem if someone is modifying the animations and forgets one of the groups.I'll take a look, it's better to fix it in the source rather than implement some workaround don't you think?
If it can be fixed easily, it's probably better to merge the groups in the mesh, but it's not difficult to handle in the animation code.