I remembered a point in the post-game MS quests where Minfilia remarks about Alisaie staying behind at the Waking Sands with Urianger. At the time it made no sense to me, because I had yet to start the Binding Coil questline. So while it may have simply been a continuity error, there's already a small precedent for side-stories being referenced in the Main Scenario quests regardless of their completion.

The Crystal Tower is probably the most prominent new landmark of ARR, so seeing it written off, along with a promising new character, simply to tell Cid nan Garlond, of all people, to "build a brighter future" seems like a bit too much wasted potential, especially since the "close ties" it was hinted to have to the main storyline have seemingly yet to materialize. Seeing it play a major role in Cid's motivations in Heavensward seems likely, at the very least.