For the record, the NieR universe does take place in an alternate future of the real world that diverged around the turn of the millennium. (The Drakengard series does the same, but around 1300, if I remember correctly.) The last ("joke") ending causes the protagonist and ultimate antagonist to crash into Shinjuku, Tokyo, leading to the White Chlorination Syndrome that necessitated the Gestalt Project in the original NieR and all that came after.

That said, we have zero context regarding anything in the YoRHa: Dark Apocalypse raids so far; nobody has any idea what's going on, and relying on Automata for context will probably not work out. (I'd like to believe 2P is genuinely heroic, but that's just bias on my part - her history and motives remain shrouded in mystery, and my expectations could always be subverted.)