Hmm, I mean... I don't really see this as being a Xenogears origin story. The story is already really different from how that would have went. I guess this could be a re-imagining with changes to the overall storyline. Or it could just be some cool concept he came up with like how he thought up of the world of Xenoblade initially.
In any case, I can't wait to see where this game takes us story-wise. I'm expecting lots of good twists and turns, the past of a character being shrouded in mystery until near the end when all is revealed, etc. And of course, lots of religious and philosophical references. All that good stuff.