Ideally everything possible could be moved into a side quest, hopefully they can try that in the future. Although I think some trims cannot be done like that as they're done within the quest.
On the quests that would go out of sync I actually believe SE could get into using Echo more. Place a flickering sepia like npc with quest marker to represent echo quests.
A. Echo quests could tell stories you were never part of, which could be neat (great chance to tell stories normally not possible). Perhaps with an echo growth mechanic (experience manipulating your ability), so you can interact with the echo to learn things otherwise not possible (excuse for exp / fighting monsters, though it wont be timetravel just a high powered version of temporarily altering a potential reality, or echo beasts come after you.. that could be a new enemy type lol).
B. Slap stuff like this into that. You skipped the moment to play imp games? Can remember it later, just come back to it.
C. Changes over time that are community based might take advantage of this mechanic, allowing people to say for example see Ishgard restoration partially done (and interact with those entities).
Would need to make a difference between when you are generating a temporary alternate reality vs remembering something you just leap frogged though. For example coming back to do the imp side quest would be a memory you just kind of let slip through the cracks lol.
Also all of those sort of goes on my own fan theory on why we're timeless, which is just that we exist in an almost out of time state- so we could technically be helping one individual in one area and doing the same in another at the same time. Which also might go along with our endless stores of anima, when we are appearing somewhere we are not transferring our anima like a standard teleport everyone else does, but just rather appearing at that time in that location, one of multiple entities of ourselves that exist as a collection. "Why the heck would you think of all that?" lol. Mostly because we have a time bubble sort of issue, and my thought was perhaps not a time bubble exactly for everyone else - just more that we're timeless. So you might be doing a task with someone in the year 1050, and then the next hour working in 2060. There are a few quests that do have this out of order effect, if you do them that way, so just my thought on all that- is we're uniquely broken / out of sync. Sort of a our player is a Tidus of Eorzea like concept (well he was a dream, but the drift of that idea of being 'off'). Maybe go as wild as to say we're the echo itself manifest- birth driven by the mother crystal beckoning us to form, because why not..lol.
Oof. XD