I'm going to talk more general here so I don't think spoiler tags are necessary.

I don't think Yorha raid series will be canon to ffxiv story at all but I also have a hard time finding something else on the First that could fill the 24 man space, on the Source sure plenty of areas but the First not so much, The Empty is being handled by Eden raid series so not much left besides Ronkan Ruins maybe.

The fact it is on the First and only we interact with it amongst the scions allows it to be more free reign to do what it wants, I can understand people not liking this as how does it fit? On the First I don't think it fits well at all, had Yorha been on the Source it would be a lot more believable due to the Allagans but it would then have to have the caveat of it must 100% fit in and Yoko Taro would be forced to be reigned in a lot more and given a lot more limitations which may have hurt people's current enjoyment of the series. Yoko Taro has said it is canon to Nier Automata in some way, we still don't know how, it has never been stated this raid series is canon to FFXIV's story.

I like to point out something from the MSQ that happens before you can do the Nier raid, Mt Gulg is lifted up off the ground. Does anyone know what would happen if say Mt. Fuji was to suddenly be lifted into the air and how that would affect the surrounding area? I doubt it because it will never happen, so would it not be possible that once Mt Gulg was lifted up by Vauthry it could cause a tectonic shift collapsing other areas revealing the factory from being underground to now being the top layer? Possibly.

You got me on the bunker parts something like that would stick out even if the sand was as high as the structure parts themselves, they stand out as metal.

People were wanting a Nier crossover event and SE delivered on it and gave more than other ones that tend to be disjointed from FFXIV but they gave it the 24 man series in the expansion on the world that the least amount of characters are affected(only the scions have the full knowledge of the First on the Source), I don't think Yoko Taro would be happy with just 2/3 quests for his characters to blip in and out in a crossover he wanted to tell a story here and it just follows his way of story telling which is an acquired taste to be sure.