The optional stories are still canon - it's just that canon will twist itself sideways to refer to a non-canon version of events if you didn't do it yourself.

For any version of the story that comes from outside of your personal view within the game, such as the lore book's summary of events or the "Tales From The..." series, the side stories have definitely happened. There is no question that they have.

Even when they are not enforced, everything points to them happening. Alisaie sets off on a journey at the end of the Binding Coil and her re-entry to MSQ in post-Heavensward mentions that she's been on one.

Even pre-Shadowbringers, CT was a piece of Cid and Nero's ongoing story - and the first time we'd encountered Nero as an ally, not an enemy.

Alexander and Omega are critical to the background of Shadowbringers, even if the game doesn't force you to do them here and now.

Warring Triad gives more detail on Meracydia, Allag, the Thirteenth and a little more insight into Elidibus. Certain details tie into what we learn in the Lv70-80 role quests.

Eden is heavily linked to the MSQ, to the point that they had to note the Scions' departure from it before the final act.

Not everything ties into MSQ, but there is a clear precedent.

TL;DR: All side stories are canon and happen at the point in the MSQ where they are unlocked. This is the writers' intent, even if they won't actually force you to complete them unless it affects the current state of something MSQ-related.