MSQ

[Iscah]

Seeing how many plot points come out of THOSE "side stories"

Unukhalai's entire existence, the backstory of the Thirteenth, the Dalmascan Resistance which cameos in the MSQ and returns in Bozja, the whole Alexander and Omega storylines which become relevant in the Twinning and as such are relevant for ShB backstory... Heck, Eden itself follows MSQ by responding to the events of 5.2 and 5.3.

I feel the MSQ would benefit from acknowledging them instead of trying to write around them.

The thing there (which would be improved by making them MSQ) is that the writers don't pretend something has happened if the individual player hasn't done the optional quest yet, so they can't rely on it as a previous event.

The exception with that approach is...

of course the Alexander and Omega raids (and CT at the time 5.0 released) but that's because of time convolutions meaning they don't need to have happened yet as long as they happen at some point in the future.