I would think the number of materials would cause the draw calls to skyrocket.
I think the same material appearing multiple times is from when you stagger the draw order of images coming from different atlases.
Like when the atlas sources in the draw order goes 1, 2, 4, 2, 1, 2, 3, 1. That would be ultimately slower than 1, 1, 1, 2, 2, 2, 3, 4. So even if you only have 4 atlases, it can end up having several materials in the mesh renderer and more draw calls, which can slow your game down if you have enough of those complicated skeletons.
This is true for pretty much any game engine and framework nowadays, not just Spine or Unity.
Are you separating these large textures into different atlases so you can mix and match from a large collection parts?
I can't imagine where the GC problem is coming from though. I don't have Unity Pro myself.
The only potential GC thing I see is AnimationState making and orphaning TrackEntry objects every time you switch an animation. If you're not switching animations a lot, this shouldn't be a problem at all.
Let's see what Nate or other users have to say.