The only fights that could really be considered "non Canon" would be Minstrel's Ballad fights which are specifically tall tales. Unless specifically stated otherwise, there's no reason to not accept most events in game as Canon. More specifically, nothing in Omega nor Alexander contradicts other Canon and as brought up, elements from both are involved in the Twinning.

As far as "Alexander exists whether we interacted with him or not..." The timeline where we interacted with him and stopped the Illuminati is the timeline he chose. If we never appeared to stop the Illuminati well... "Canon" becomes the least of our worries since we'd have a goblin army running around in a mobile fortress doubling as a time God lol

TL;Dr it's strange to claim only Bahamut raids are canon and to have one throwaway line as evidence, but then turn around and refute an entire dungeon dedicated to Alex and Omega as evidence that the other tiers are likewise canon.