One possibility, the machines realize that ( at least for the present ) they can't afford an all out war with their makers. Understanding humans might be important to the machines, either as a way to avoid war or as a way to become self sufficient. Therefore, Favre is offered to humans as an interface with humanity hoping that both "species" learn from each other. Allowing communication with Favre and covering up his origin are logical developements if the machine's goals are to be met. Anyway, that's my take.