James Madison had no part in drafting the 1790 Act. You can not claim that he “thought that the Congress had the power to define Natural Born Citizen”, that is your speculation.
If he didn’t think that the Congress had the power, he wouldn’t have taken the same course in 1795, would he? He might have turned to the Supreme Court. That option is still open to the Birther Brigade, they can challenge the law in court. Instead, they have cited the Birther Brigade canon and the judges look at the facts and the law, wonder why these amateur legal brains have not talked about the law and it’s over.