What is canon and what is not (Spoilers)

[Melichoir]

My understanding is that more or less, if it's handed to you by a quest giver and isnt a Cross over Event - its canon.

If you want to be more nuanced, MSQ is hard Canon. This is the undisputed story, but it will take liberties in assuming youve participated in certain side events at times.

Side Quests, Beast tribe Quests, Raids, etc are all soft canon events and they exist more to flesh out the world and explain some of the things going on that influence the MSQ. You dont have to do them, but they do impact your understanding of whats going on in the MSQ and the world at large. There are admittedly inconsistencies in the timeline of things, but that is just the nature of playing an MMO. Not much you can do about that.

As examples: CT, Alexander Raids, and Omega Weapon help fully explain how ShB can even occur as technology from these events allow for the creation of the tower machination that makes the CT go to the first in the first place. If you havent done it, it is implied you know about it and the MSQ kind of glosses over this. But these events do take place one way or another, regardless of your involvement.

Event Holiday Quests are incredibly loose canon. They do happen and the NPCs will recognize you if you do the event repeatedly through the years, but what happens isnt reflected in MSQ or indicative on how much time has passed. It's almost like Holiday Quests are in their own separate timeline from the MSQ. Holiday quests may reference MSQ stuff loosely on occassion, but very rarely do the actually impact one another.

Cross Over Quests are canon in name only. They dont affect MSQ or seem to have any real world impact on things. These are purely cosmetic sub mini stories and games.

[Iscah]

If you want to be more nuanced, MSQ is hard Canon. This is the undisputed story, but it will take liberties in assuming youve participated in certain side events at times.

Actually it's sort of the opposite. The "undisputed story" as intended by the writers includes the optional events.

Meanwhile, it does not assume you've participated in events if you haven't - this is where canon starts to twist itself according to your individual game progress.

The canon version of the Binding Coil, for example, ends with Alisaie inspired to depart on a journey of self-discovery. When she rejoins you, she makes reference to that time you spent together.

If you haven't progressed the Coils storyline by that point in the MSQ, she will instead mention your partial progress, or maybe that you haven't met since you first encountered each other early in the game, and she's been on a journey for some vague reason. It's a less satisfying version of events, and it's not how the story is supposed to go, but the game will do its best to alter the dialogue to your individual situation if you don't look too closely at the rough edges. It's only meant to be a temporary non-canon version of events until you see how the story actually played out.

Of course, this approach only works because Alisaie isn't visibly in any different a state whether you completed the story or not, so the difference can be swept over with a few altered lines of dialogue. If the state of something has actually changed, the MSQ will probably avoid referencing it - but may make the earlier quest a prerequisite if it's necessary.

On your hidden paragraph (spoilers up to 5.3):

The CT/Alexander/Omega trio are a special case because of the time travel element. The game is not pretending you have done them by the point that Shadowbringers takes place - only that they will have happened by the future point that Cid needs the information to develop his time machine concept. This is why the game can treat them as definite fact without requiring you to have done them first. If you haven't done CT during 5.0 then the Exarch will say that you haven't met his past self yet.

Again, the reasoning is quite flimsy if you look at it too closely and it all makes a lot more sense if you did the other stories when you should have, but their route around it is not pretending that you've completed them.

Note that the Crystal Tower alone has become mandatory as of 5.3 - not because of its importance to Shadowbringers' plot but because it is absolutely necessary for those events to have happened first. You cannot find G'raha Tia asleep in the tower if he hasn't shut himself in there first. If the writers simply pretended you'd done things when you haven't, this wouldn't be a problem - you'd simply find him there whether you'd ever met him (in that form) before or not. But that isn't how the story handles things. The sequence of events must be that you meet G'raha, then see him shut in the tower, then get him out again. You can put it off but you will not see those events happen out of sequence.