I haven’t used much of a muscle system…but I’ll try to help here. If you want to do something like corrective blendshapes, you can set those up in MB, it just takes a character face and a relation constraint…if you’d like me to go into more detail I can.
Because I’m not real familiar with how to set up a muscle system in Maya, I’m not sure if you can do it in MB or not. There’s a lot of things you can recreate with a relation constraint or expression constraint in MB, so it could be possible. If you could give me an idea of how you do it, I might be able to help you figure it out.
But if you set up things like influence objects in Maya using expressions I would think you could set them up and when you reimport animation it should work just fine. MB won’t read the expressions, but since merging animation into your scene file should only affect your skeleton (in theory) and your skeleton would drive the influence objects, I would think it would work. You just wouldn’t be able to see the results of the influence objects in MB, but they’d be there when you render.
I know I wasn’t able to give definite answers…but I hope I helped a bit! 