I think you're overthinking things a tad. This game doesn't seem to have nearly as complex a story as you are making it out to be. Or rather, it doesn't take its story that seriously. Stuff just happens and that is that. The party can alter time at free will but somehow they are never affected by this I am told.

You're also dropping a text bomb about the whole cosmic scheme of the game and I'm not even halfway through it so....