Right, then... [Nier: Automata/Copied Factory] [Spoilers]

[Nalien]

I'm going to go out on a limb and say that our dear friend, the Crystal Exarch is to blame; He magicked a whole Crystal Tower from one world to another, through time too, no less. How absurd is it really to imagine that a chunk of another world (a splinter timeline from Nier: Automata) somehow got mixed up in the whole process as well? The whole process of just summoning us to the First was very trial and error, with the Scions getting mixed in precisely because this was uncharted magics, so an unexpected side effect of transporting Crystal Tower through time and space? Easy enough for me to believe, and handily explains away things like the Copied Factory somehow being hidden for so long. It wasn't hidden, it merely got plopped into the First the same as Crystal Tower, at an unspecified date. It lay undiscovered because post-Flood people probably weren't in the adventurous mood, and it could have materialized in an area that had previously been mapped out as wilderness, so people just assumed it was still wilderness and had no reason to go looking there.

Now, it would require XIV to exist in some kind of gaming multiverse, rather than its own little bubble. Previous cross-over events have already established that, though. If Shantotto can magic-mishap her way from Vana'diel to Eorzea, then yeah... G'raha can accidentally pull elements from a failed Nier: Automata timeline with him as he Dr. Whos' Crystal Tower from his own failed timeline. If all previous cross-over events exist in their own little Hildibrand-bubbles for you, well then the Nier cross-over is no different? Just because it's a 24m raid doesn't really change that IMO, not until they pull it into the MSQ somehow, but I'll cross that bridge if and when we get to it.

Of course, Yoko can just make up his own reasoning as to why Nier popped into XIV. Or he can give no explanation whatsoever. Crystal TaRDiS is just my theory on it, I kind of expect we'll not be given a clear reason as to the how or why of it.