The idea is that Vedal plays as 2B, so he's in control of most of the game's progression, but Neuro can still mess around without too much consequence ||and lock Vedal into one of the joke endings because she keeps massacreing Pascal's village||
And maybe for routes B and C, they can switch roles with Neuro at the helm. Hopefully she'll have learned to play the game through watching Vedal, but knowing her, she probably won't.
I have no idea how feasible this even is with Neuro's game integration. From what I understand, NieR:Automata runs on a proprietary engine, but the modding scene saw a breakthrough in 2022 with the Church thing. I think it's a cool idea though.