Welcome, DanielWolf! 🙂
You're right that generating an entire skeleton would make it difficult to get the animation into an existing skeleton. It could be possible using Import Project, which allows importing an animation from another project file. Rhubarb would write a skeleton JSON file, then you'd need to Import Data to get it into a project file, then you could Import Project to merge in an animation. Note this requires both skeletons to have the same objects that were keyed (slots, attachments, events, etc).
Your proposal would work fine and is simpler than the above juggling. Users would export their project to JSON, add animations to it with Rhubarb, then they can use the data as is or import it back into a Spine project for further editing. I don't think there is a better approach.
