Remember Noah?

[Iscah]

She shows up as soon as the Crystal Tower quest chain is complete, with the implication that Koh found Noah's prison prior to the sealing of the Crystal Tower. By the time the quest chain is complete, they would have already completed the 'merger'. If we aren't the ones to have found her first, they could make it so that our new friend did in the MSQ, if we have not completed that quest. She is standing right outside, and given his experience AND given who he is, he might have noticed her presence.

That's not how the game handles optional quests though - there will never be a version of events where someone else found her first. If they were ever going to build on it, we personally have to first go through the quest where we meet her and learn her importance - essentially stepping back in time to 2.5 as we do so.

It's the same logic why the Crystal Tower became required for 5.3 - it needs certain events to have happened first so the plot makes sense, and you are the person who needs to make them happen.

(I'm not sure how the timing of Noah possessing Koh is relevant either way - of course it happened prior to us meeting her, even if we did it immediately after the tower was sealed at the end of the main quest line.)