Sometimes life isn't fair.
And sometimes a sad ending is a lot more impactful to a story than a happy one.
She will get her big character story arc with the shard travel and probably some hidden knowledge she finds. Most likely she will be out for a few expansions and comes in as the lead when we go to another shard.
And funnily enough, popularity polls say this isn't actually a reason. She's not the most popular Scion, the most popular female character, or the most popular female Scion.
It's funny, because she looks like she would be. If you're coming from an assumption that FFXIV has a population breakdown similar to something like WoW that skews a little older and much more male-dominated, yeah, she seems like she'd be a shoe-in for being one of the most popular characters and you take that as a given; I'd have probably guessed her and maybe Raubahn would be the big players if you made me guess early on. But in truth, the audience actually skews much more female-dominated, younger, and has tastes that mostly skew towards more recent characters, and (to be a little bit comically reductive) Cute Boys. As a result, while Y'shtola competes fairly well as far as ARR-era characters go, character popularity polls put her pretty firmly below the likes of Emet, G'raha Tia, Zenos and Alisaie.
Pretty much what I expect. She's already implied that the First is only her first stop (no pun intended) - she intends to explore other shards and find out the mysteries of the world. Will she reunite with Runar? Oh almost certainly. But I don't think she'll stop there, as she has pretty much said as much, and I can see her coming with us to a new shard, whenever that happens.
I don't think any of the Scions will die, not after all the death fakeouts and Ultima Thule in particular. It would lose all its impact at this point.
Yshtola has likely achieved imortality unless they do go with the "clean cut" and start a new cast of players.
Shes even in other FF games by now. I do believe at one point she was on the list of "going to die" we had Red flags from ARR throught every single expansion, but she always comes out fine and usually stronger.
Ah, yes, in a firm crowd of lively faces like Tidus, Aerith, Noctis, and Jack Garland.
I don't really think the logic of 'she's in crossovers so she's important' makes a lot of sense in the first place, but even if it is, let's not pretend that 'being in FF crossover games' means a character is a static, undying icon.