Spine-Unity just generates a mesh and uses a Material to render it.
As long as your material settings are coherent, it should render fine.
If it requires you to set something manually on the Material, you should do that. And it should work fine. The Spine runtime shouldn't really care.
Note that if it's a straight alpha, you may have to disable "Premultiply Alpha" under "Advanced" on each SkeletonAnimation. It will be disabled by default if you don't use any of the default Spine shaders.