As far as Automata placement
I don't really feel like it syncs up to Automata.
If it's after Automata, then as said above the comments about machines feel weird. If it's before Automata, it's weird that the red girl would be there without being commented on here or in Automata.
I am at least glad that it seems the enemies didn't come from the Arc that shot off in ending D of automata, but rather seem to be from something separate here. The 'machines' we encounter might not be the same ones from Automata and just copies made by the seed or something, just as it seems the 2B and 9S we met were copies made because they put their data into the seed. And the dwarf with us in the final raid was a copy. So I don't think this is the same 'Red Girl' from Automata. Just as the Knave of Hearts we encounter isn't the same creature fought in Replicant etc.