I'm quite new to Unity to be honest, but apparently you can apply a different material to each sub mesh. Guess I'll read more about that.
Edit: Using sub-meshes works, but it basically keeps the draw order: Material 0 -> Material 1 etc.
So you can either create them based on how many different atlases you need to use (2 atlases = 2 sub-meshes), or have each bone as a sub-mesh which allows you to keep the right draw order.