The Reunion Files says they were already thinking of a sequel for FFX in the first place, hence the ending.
They just hadn't figured out which medium they wanted to do it in. So they tried their hand at making a little sequel cutscene to gauge interest. Cue, "Eternal Calm." People liked it, cue FFX-2. People loved it, cue interest in doing more sequels. And the Compilation was born.
It makes perfect sense, because in essence, Tidus is a living aeon. The reason he vanished in the first place was because the Fayth didn't bother to think "Oh hay guiz, lets give a gift to the gurl who saved the world two tiems by reconstructing her imaginary b/f and bonding him to her love so that he'll always exist so long as they love each other <3"
An aeon is manifested due to the strong emotion, feeling, thought, etc that fayth "dreams" into existence and allows for a summoner to invoke via pyreflies. By the Fayth reconstructing Tidus and allowing Tidus's dream to exist along with her love he exists. It's romantic and sweet. Big deal.