I don't think I should have to understand all the nuances of the root bone to use spine. It sounds like the root bone also means too many things and has conflicting uses. Anytime I find something like this in my code I know I'm asking for trouble.
I think all the runtimes should support positioning a skeleton in the same way they all support positioning sprites or whatever objects they have in their engines. Its not really productive to have to understand the way spine does positioning so I can then position the skeleton where I want it to be. At that level the skeleton should just be another object not something that I have special understanding of. I also think you are asking for a support nightmare if everyone has to write their own "make the spine skeleton position correctly" in my game engine code. There will be an endless supply of forum posts asking why my skeleton is not positioned where I want it to be. And please don't get me wrong I know I can figure out how to do it no matter what you provide but you really probably know better than me how varied the spine user skillset is going to be.
For example, in Cocos2d, I should be able to set the position and anchorpoint of the AnimationNode just like I can any other node and the skeleton should work like I expect. So if I set the anchorpoint to 0.5,0.5 and then set the position of the AnimationNode to the middle of the screen the skeleton should be centered on the screen.