I understand what you meant, I had a similar client where in we had to make multiple skeletons according to the attachments like hats, clothing, hair etc, all separated from the body skeleton (base). they work together as long as the animations of each attachments are identical to the base (body skeleton)
While working on mixing and matching the files, we have this master file wherein all of the skeletons are visibly present. just to make sure animator can check if they all work together.
after that, they'll all be exported separately so each attachment has its own respected atlas file.