Why Eden is not MSQ?

[Dualblade]

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.

The Crystal Tower (as well as Alexander and Omega) aren't a matter of if the WoL was present, but of WHEN they were present. The implication is that your WoL WILL do it, or would have in the alt future, at some point. The question is just whether you had already done them all already or if it was at some unknown time in the soon to be future.

[Ceallach]

Potential spoilers ahead.

Have you been through the Twinning and all of the main scenario quests? Then you know Cid helped deal with Alexander and Omega with or without the Warrior of Light, and his vision made it possible for scientists after him to manage inter-Shard travel. Therefore, while not part of the main scenario quests, the events surrounding Alexander and Omega are canon. If you're a summoner, it's pretty clear the events surrounding the Binding Coil of Bahamut are also canon, even if you personally hadn't bothered.

So what's the big difference between Eden being side quests instead of main scenario quests?