The problem with the "it's just Bones and Scotty telling a story" theory is that they know too much about the MU if true.
Assuming they're just making it up as they go along, they don't "know" anything. They're telling a fairytale, nothing more. It could be anything. It's no more far-fetched than, say, the existence of "Earth Prime" in DC Comics, which was basically a copy of our own Earth where most DC characters were fictional comic heroes.