This might be a question for the official Unity forums. Spine will treat/use textures normally as long as the Material is correctly set up, since all Spine does to render is generate a mesh and use the material information to render that mesh.
At runtime, it manages which materials a SkeletonRenderer needs to use, but not the contents or settings of the materials themselves, including texture settings.
The Spine-Unity texture importer automatically sets texture import settings to "uncompressed" for standard sprite-quality results, because otherwise, textures are imported as "compressed" which greatly degrades the quality of the alpha-blended textures.
Its compression is really better suited for 3D meshes, where geometry and lighting are better able to define the forms.
But you can remove that automatic setting.
