In Dissidia, each playable character shows up after the conclusion of their story in the game(s) that they originate from. This is done as to ensure that the canon of their origin points is not disrupted and altered. In other words, Y'shtola isn't rushing off to fight in Dissidia in FFXIV's present canon. She does so after FFXIV's story is concluded...which isn't going to happen for quite some time. One thing it does imply, though, is that Y'shtola is unlikely to be killed off in FFXIV.

If we did end up getting a Dissidia crossover event then, ideally, it would have to be explicitly non-canon.