If I’m understanding you correctly, then it’s the 1st option - make the desired skeleton and import it as a skeleton asset to the engine, then it’s a matter of weighting both models separately in Maya. “Copy smooth skin weights” is the most basic way to get your skin weights from one mesh to another, but it’s just about guaranteed you’ll need to do some cleanup on the transferred weights unless the models match very closely.
If your models do happen to share the same vertex order or UV mapping, there are options in the tool to transfer in UV space which would give more consistent results. Works best for things like heads or arms where the maps can be shared.