I Believe tha advantage of motion skeleton is to quickly create a mechanism without investing time in solid modelling, especially useful for new concepts (of which you actually DO know how you want it).
perhaps you can share a bit about what kind of mechanism you want to work simultaniously with copies?
What do you mean with external references when mechanism was suggested?
I use mechansim all the time in large assemblies and I would use eg. a servomotor or initial force from the skeleton model to have eveerything work simultaniously in the main asm.
There is actally something in between: "mechanism connections". You can only create these in mechanism but they remain active in normal mode; eg. gears. You can link connections in the main asm using these, the motion skeletons dont even have to line up to be connected!