*Spoilers* Questions about Shadowbringers

[Iscah]

I am speaking of how the MSQ handle the view of things, Not how CT handle your progress in MSQ.

I'm also talking about how MSQ handles it.

Once you have completed CT, there is no ambiguity about when it happened. It happened prior to Shadowbringers, and your character knows G'raha Tia prior to meeting the Exarch.

Your progress in the Crystal Tower storyline permanently alters the details of the MSQ that follows it. But your progress in the MSQ has no effect on the Crystal Tower.

The CT story is never intended to take place at any time other than post-ARR. It cannot. Even if G'raha Tia was a one-shot character who never came back, and all this time business never happened, the CT story is still set in a designated point in the MSQ because it forms part of Cid and Nero's story. It happens prior to their interactions in post-Heavensward and the Omega storyline, even though it's possible to play those first and then do CT afterwards. That just means you saw their interactions out of order - not that you changed the order in which those interactions happened.

The important thing is, the game will not acknowledge those earlier events happening unless the player has seen them. It doesn't change the sequence of events, but it does affect whether people will say at the time if those events happened or not.

All quests are supposed to have happened at the time they became available to you, and the story doesn't actually support "multiple sequences". Early events affect later events, but completing later events first does not have any effect on the early events or when they happened.