Once again, Mama's drama queen tendencies only show through when she is actively taking part in the story. Instances of her acting solely as a narrator, of which there are several, see those elements completely removed. Additionally, the FFXIV crossover is, and I stress this, not part of NieR Re[in]carnation's storyline. It's simply a thing that is there in some form, and while presumably also canon to that world (as the NieR raids were on FFXIV's end, per the terms both teams agreed to), it's not something relevant to game's overarching plot at all. It's also not really being told from Emet-Selch's point of view. He is the character upon which the story focuses, but he plays no part in its actual telling outside of being one of several "actors" involved. That was kinda their intention with the crossover - it was to be his story, not necessarily that of the ancients. Not a story he participates in telling, but the story of his part in things. The crossover announcement and promotional materials corroborate.
It stands to reason those things, which were part of the world prior to its division, would remain in some form afterward. I'd have been more surprised to learn they were for some odd reason absent. I do find it logical they were unstable enough to require supervision immediately following the Sundering. Perhaps less so time since it's something of a universal constant (gravitational influences notwithstanding, of course), but I suppose that comes with the territory when you divide something into fourteen separate yet connected dimensions. It tracks that a blatantly unnatural event would have equally unnatural consequences.
I'm not seeing the conflict here. We've ample reason to believe the sundered were in extremely poor condition immediately post-sundering, but that doesn't mean they would remain as such forever.
So if you consider the crossover event of no count, what do you consider acceptable sources other than FFXIV itself?