NPCs with plot armor, does it bother you?

[Iscah]

Technically Ishgard still fights dragons in FATEs or such despite the war ceasing, but yes seeing Estinien alive and well would be jarring if something happened to him.

The thing is, it's still jarring even if he is still alive at the current point in the story, because Estinien-in-the-dragoon-quests is clearly not the current rogue adventurer who's trailing us in Stormblood, but a past version - the Azure Dragoon wielding the Eye of Nidhogg, even if we've 'already' seen him abandon that title and the Eyes have been destroyed. We've stepped back in time while we're playing this part of the story.

At the point of the story where Estinien was possessed by Nidhogg and we were potentially going to have to kill him, I wouldn't have thought "that can't happen because he needs to still be around for the ARR quests that happened earlier". The time bubble makes things a bit flexible but you can still say that some events definitely take place before others, and I would expect that a character is really only 'shielded' if they need to remain permanently in place somewhere to give optional quests - and Estinien doesn't, as far as I can remember. I don't think there's any point in the dragoon quests where he's left to stand around or give you quest objectives - he'll arrive for a scene, leave again and then you talk to Alberic or do some other objective to progress the quest.

(On a similar track - yes, Nanamo ultimately survives that assassination attempt, but you could still complete the Lv50 CUL quest at a point where she's allegedly dead / actually in a coma and definitely not available to come for lunch either way.)

Overall I wouldn't see any character's involvement in a quest plot during Expansion A as any guarantee of their safety during the events of later Expansion B. It's only if they need to be available to give out quests that can be picked up at any point, like Urianger, that I'd expect them to definitely survive in other storylines.