I had a bit of a shower thought on the YoRHa raids.

In the final raid, 2B and 9S repeatedly push the whole "Machine Lifeforms are just random, don't think about it" stuff, which is part of the reason I'm hesitant to say the FFXIV stuff comes after any particular ending from Nier Automata—that particular cherry gets popped really early on, to the point where it comes across as willful ignorance or outright lying. On the other hand, they don't seem particularly phased by anything that happens in the raid, up to and including the appearance of the Red Girl, which afaik is the "physical" manifestation of the Machine Network's intelligence.

But in contrast to that, at the start of the Copied Factory 2P answers the same sort of question by giving an accurate summary of what the Machine Lifeforms' gibberish means. Maybe I'm just giving the writer the benefit of the doubt, but in hindsight it's a pretty early sign of 2P's true allegiance.