egg-optchar can remove joints from an animation that are not used. For instance, it will remove the leg joints from a hat model. Of course, when you do this, the hat model no longer has the same skeleton hierarchy as the whole character, so it means you will have to replicate out the animation tables. You can have, for instance, a copy of the animation tables for hats, and another copy for coats, and another copy for pants, and another copy for the overall character. This will at least avoid the need to redundantly compute every single joint for all the pieces of clothing, at the cost of additional memory to maintain modified copies of the animation tables.
But this isn't what you're asking about. You want to load multiple different identical skeletons, each with its own geometry, and then merge the skeletons into a single skeleton that only has to animate once. This is actually supported, using the mergeLODBundles flag to the Actor constructor, but it is meant to be used for different LOD's of the same model, rather than different pieces that are all visible at the same time.
It would no doubt be possible to finesse this system to also support different pieces that are all visible at the same time; you'll have to be able to read the Actor code and understand how it uses the low-level Character and AnimBundle interfaces. Since you've been working in this space already, I think you've got a pretty good shot at this.