You can have multiple retellings of the same story across different types of media that are inconsistent with each other yet still internally 'valid' or 'canon' (i.e. TV series vs. movie plot). This prevents you from using one to draw inferences about the other, however.
Mama's standalone story about a powerful mage and the destruction of his society by warring gods is perfectly valid within the framework of the NieR Re[in]carnation universe, which is what the adaptation was designed for. It doesn't need to be internally consistent with anything else. Trying to draw conclusions over in FFXIV is a different story, however, and not just because of the contradictions with the other soul splitting examples that I've already described. If Elidibus was piloting Zodiark into battle at the time of the sundering, Elidibus would be sundered as well. That detail doesn't really matter in the NieR retelling, because Elidibus doesn't need to exist in that story. Likewise, the in the NieR retelling, the Final Days are described as being caused by meteors that rain down to destroy life on the planet, and the sundering itself is depicted as an unintended consequence of the battle between two gods, because neither Meteion nor dynamis feature in this version.
You don't need to resolve any of the contradictions with other versions, however. It's just a retelling of events with some variations on a theme mixed in, much like DSR was.
As far as FFXIV is concerned, I did inquire around how the mechanics around sundering work during the last lore Q+A, especially in the context of the other soul splitting mechanics that we've seen. I don't think we'll get a clear answer, because there's probably no clear set of rules around it currently. I think the best explanation that we have is still the one that Emet provides in the Ocular, which is why we know that sundering something doesn't cause physical damage and is akin to a sort of cloning process.
I get that there's a need to try to explain how people dispersed from Amaurot and why they didn't try to stay and rebuild using their old tech. A 'Babil' story is likely necessary to explain this diaspora. The only issue is, they haven't actually told that story yet in FFXIV, so this all ends up being very speculative.