The more I think about the twist, the more I like it. The entire series has been about living up to preconceived legends. Solid in MG1, Raiden in MGS2, and Big Boss in MGS3. Each of them were normal soldiers who were put in extraordinary situations and expected to become greater.
It would make perfect sense that we'd see a body double become "Big Boss," especially with all the soldiers backing him up and treating him like a legend. What I hope Ending 3 explains further, though, is why Big Boss became evil.
I'd always figured it was because of the conflict with Zero, and that he wasn't evil he was just on the other side of history, but it sounds like the battle with Zero might not even be a thing anymore.