I understand how it works, but I've also seen it handled differently in another MMO, to a point where occasionally when new low-level content was patched in, it would feature token appearances by characters who "died" later in the storyline. Not saying it was the most elegant solution, but it did allow them to keep a myth-arc going across more than half a dozen end-game raids without the "continuity gating" that FFXIV seems to be so in love with. People who don't care about the story didn't care, and the people who did had extra incentive to go back to lower-level questlines they might have overlooked.

The only story I'm really invested in seeing picked up again could very well just end up used as a continuity gate later on, considering everything that happened with a certain mad scientist seems almost too important to leave entirely optional, but I'm fully aware of the problems that will cause in the long-term, so I hope they can find a more delicate solution.