Why Eden is not MSQ?

[Iscah]

There is a high chance Eden may become one of those "will happen no matter what" events with the only difference being if WoL took part in it or not.

For Crystal Tower story we know it happens no matter what but the difference is that WoL did not get involve or did get involved in team NOAH.

For Eden's case it may focus on Ryne, Thancred, and Urianger resolved Eden's events without WoL's help if WoL "choose" not to do Eden Raid thus anything Eden related will then only mention Ryne, Thancred, and Urianger but if WoL does take part a 3rd Dialogue option opens that will result in a alternate dialogue including WoL.

They are exploring Alternate Dialogue paths now with 5.0 expansion which we see in the MSQ.

As Dualblade said, that isn't how it works. They've been "exploring multiple dialogue paths" since right back in ARR, and no quest events ever happen without us being there. If you skip an optional-but-important storyline, later quests will not claim those events happened, and may outright indicate they haven't.

If you haven't done the Crystal Tower, the game does not - cannot - assume it happened and you weren't present. You need to be there for that part of G'raha's storyline, because he remembers you being there in his past, whether you've personally been through it yet or not.

If you haven't done the Crystal Tower yet, variable dialogue reflects that. The Exarch tells Urianger that you are yet to meet his past self.

At the same time, CT has a designated place in the storyline, and completing it post-Shadowbringers would "slot it in" to that earlier time rather than adding it afterwards - as long as you tick "reflect quest progression" when you rewatch the cutscenes.