Welcome to the community Mike 🙂
Yes, you can start with a skinned skeleton. There is no inherent requirement that Ziva VFX be solely used to simulate anatomical correctness, as It is a general purpose elastic solid simulator.
(For example, we have customers who have used it to simulate jiggly cartoon characters)
Regarding rigging the scapula, there are a number of different approaches that could be taken . . .
One approach that we have used in the past has been to create additional stiff zTissue versions of the scapulas that are goaled to zBone scapulas. We then attach all of the connected muscles to the tissue version, so that there is some ability to influence the scapula's position based on the force being exerted by the surrounding muscles.
Regarding how picky the system is regarding geometric inputs . . .
There is a mesh analyser that can be found in the "Ziva Tools" menu. If you run this on your mesh before to attempt to add it to the system, this will inform you of anything that should be changed before attempting to solve. (co-located vertices would be one thing that we would fail to solve provided that the overlapping vertices are connected neighbours)
For meshes that fail our analyzer, they can still be deformed along with the simulation by adding them as an additional Embedded mesh.
I hope this helps!
Looking forward to see what you come up with!
-jj