For most runtimes, the best practice is to NEVER animate the root bone. I'd say it's generally a good idea in any case, even from an animator's perspective, since you never know when you need things to move independently. It's certainly how I construct and animate all my skeletons. One level lower is not a big deal.
Some runtimes (and use cases) rely too much on being able to manipulate it programmatically, especially for scaling and rotation.
For your case, it seems like you need to manipulate it so you shouldn't be keying it.
So adding that extra bone in Spine editor is what I recommend.