Why Eden is not MSQ?

[Iscah]

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?

There isn't a difference between Eden being a sidequest and Alexander/Omega being a sidequest, but there is a difference between them being sidequests or MSQ - it affects how they can be referred to in later storylines.

The "optional" sidequests are intended to happen in the grand scheme of the story, but they don't happen without you. Instead the game waits, and rearranges dialogue that would otherwise refer to them, until the individual player completes the quest. This also means that sidequest elements and characters can't be easily brought back into the MSQ because they may have "not happened yet" for the individual player.

Time travel means that all waiting is off. The events happened, with us involved, sometime in the period between the player's present and the future point where Cid made use of the knowledge he gained from it.

The Exarch specifically says so when he explains it in 'The Unbroken Thread':

CRYSTAL EXARCH
[The concept] was rooted in a theory which unified several fundamental principles discovered over the course of the Warrior of Light's adventures.

This line doesn't change in the default "no sidequests completed" version of the scene. So, they definitely happened, and the WoL was definitely there.

But really they happened alongside the MSQ in the patch where they were introduced, regardless of when you do them, and the player is bending spacetime by leaving them unfinished beyond their designated point in the story.

For a Lv80 player who skipped the Lv50 raids, Nero is still standing around Mor Dhona in a paper-thin disguise after fleeing the Praetorium, and Urianger is still at the Waking Sands hoping he can get you to help Alisaie (who you've only met once back at Lv20) with the Binding Coil. It's not where those characters are in the story right now, but they'll stay there until you straighten out the timeline by completing their quests.