There's no need for a huge, in-depth explanation for each and every aspect of the game's story. The Omega stuff was heavy on the fan service, but it made sense within the context of the game world. The same can be said of the Return to Ivalice stuff.

Final Fantasy games have always had references and throwbacks. They don't need to all be intricately explained. It's just part of the charm. Crossover events are just an extension of that.