Ronkan ruins could have been amazing. Or a desert temple in Ahm Araeng, or, say, mysterious dwarven ruins deep in the Duergar Mountains that aren't based on another game's setting.
The fact we don't have anything to particularly point to is a circular argument, because gameplay requirements are what drives their game world design. If they needed a setting for a 24-man raid, they would have created one.
By the same logic, if they hadn't decided to make a NieR crossover then we wouldn't have the Copied Factory and we wouldn't have just had an alien spaceship (as far as I can tell) tear a hole in Kholusia.
I don't see how it's more okay to wedge this into the First than the Source. They're equally real worlds inhabited by people I quite like, and I don't want to see the First get this literally-or-figuratively alien design forced on it. Canon or not, it's made a visual impact on the game world and I really am not happy about that. At least I could ignore the Factory's existence when it's isolated.Also dear goodness Chai-Nuzz must be beside himself right now.
As to whether it's canon to FFXIV or not? I certainly hope not and that the writers will never want to reference it again. But every alliance raid up until now has been canon - one has literally just become part of the MSQ - and we will be getting it in alliance raids forever more. (As I've said previously, I find it bizarre that this non-FF game is getting a permanent feature when actual FF crossovers have been temporary events, possibly contradictory to canon, and never to be seen again.)
If it was a temporary event, I could accept the focus on telling a story that relies on previous familiarity with the characters, because it's got limited time to do its thing and it's just not targeted at me. But this is a permanent, major side story in FFXIV, which makes me feel it should be comprehensible to FFXIV players first, extra fulfilling for NieR players second. Ivalice dropped the ball on this too, but not to this extent - I felt lost but at least there was clearly a story happening even if I didn't enjoy it much.