That's true that it might break if you change the texture resolution. That's why you should make the atlases square at the time you pack them. Changing them to square in Unity instead will likely just break them. (The same thing happens when you just change the resolution in Unity)
Changing its system to support mutliple resolutions is also a bit of a problem because the atlas spec Spine is using is libGDX. I'm not sure if that'll change when meshes and FFD come along.
We'll have to wait for Nate for word on that. Maybe it'll support a proportional spec too to reduce this problem (while introducing a few others that we would need to keep in mind, I think).
As for being inefficient, that's kind of iOS devices' hardware's fault. Not Spine's.
But Unity has a plugin you can buy called 2DToolkit that Spine supports. It packs atlases itself shared between multiple things in your game (I assume in squares if you need them to be). You should look into it. I'm not sure if it solves your problem though. I haven't tried it.
Note, I'm not one of the developers, so don't take my advice as official support. : p