It is actually much more about death than X. It's not "Ah, a big thing kills everything!" It's more about "I'm on a timer, I WILL die. Even if I win against the bad guy and save the game I will die someday and I have to learn to cope with that fact."

Idk, but to me stories where you, through a character, are made to confront your own mortality (like FFIX and P3) are fundamentally much darker than just having to deal with mass-scale destruction. One is just much more grounded in our everyday lives, which makes it hit closer to home.