If it's actually common knowledge that both players are "perfectly rational" then they must do whatever game theory says.

But if the paperclip maximizer knows that we're not perfectly rational (or falsely believes that we're not) it will try and achieve a better score than it could get if we were in fact perfectly rational. It will do this by cooperating, at least for a time.

I think correct strategy gets profoundly complicated when one side believes the other side is not fully rational.