Chocobos, Moogles, Cids; The Worlds are Connected

[Tabris]

And who says it has to be on the same planet? For all you know, the Spirians could have discovered space travel, and travelled to Gaia.

I believe this is the case. In X-2, the Al Bhed-boy Shinra (!) says that he might be able to detract the pyrefly-energy from the Farplane and use it. According to the interview I read, and which have been quoted many places, he never succeeded. But his family, a thousand years later, moved to another planet (which is Gaia) and there the Shin-Ra company developed Mako.