The only thing I am seeing not is to make "reconfiguration" animations that would position parent bones. These bones would be some kind of meta bones (a meta neck, meta shoulder, etc.) that would be used just for positioning, and maybe a bit of rotation if needed.
When you switch to a skin, you have to use the reconfiguration animation so that these meta bones are well positioned.
The animations (like walking, jumping, etc.) should never have any key on the metabones.
I have not tested this yet on a project, but I guess this can do the job.