I think the whole memory wipe thing in the opening episodes seems to be the anomaly

I agree. Doctor Who has never worried about historical figures Seeing Too Much in the past, and it didn't here, so worrying about it suddenly in Spyfall is odd and, in the context of the whole of NuWho's history in terms of discussing the ethics of mind-wipes, kind of weird - why was it there? was it meant to contradict something Moffat did? is it supposed to be about how the Doctor hasn't learned this lesson? did Chibnall just forget there'd been this whole thing about mind-wipes? I don't understand!