I was thinking, maybe this could work similarly to the Dragoon quests in ARR. If you did them, you would've met Estinien earlier and your dialogue with him would be a little bit different when you meet him in MSQ. I understand the deal with the void is a bit more complicated because with the Dragoon quests there wasn't really any meaningful change (as far as I remember at least), so the story would make sense regardless of whether you did them or not. Regardless, the main argument I see against having Unukalhai show up and explaining the situation to the WoL (in case they didn't do warring triad) is that it wouldn't make sense since it was the WoL who helped him to begin with, so it would be weird to go back and do those quests after the fact. But by the same token, if you already met Estinien in the MSQ and go back to do the Dragoon quests, he still has the same dialogue and still doesn't know who you are.

If the devs are fine with this sort of weird thing happening (which, let's be honest, it's kinda inevitable) then I think they wouldn't mind doing the same for Unukalhai/Cylva.