It wouldn't make a difference since Sprites are rendered using SpriteRenderer and Spine Skeletons are rendered using MeshRenderer.
Even if they share the same backing texture and Material, these two different renderer types would still not be dynamically batched by the engine.
So performance-wise, at least outside of load time, it really makes no difference.
Additionally, there is currently both a way to load your skeleton without a Spine atlas, and to load Sprite textures into your attachments.
So if you really want to put all your sprites in one texture in Unity and have your Spine skeleton be backed by it, you can do that with a bit of extra code.