Another way to look at it is that Madison thought that the Congress had the power to define Natural Born Citizen in 1790 and he used the same power in 1795 to rewrite the legislation. This, among other reasons, is why many in the Judiciary believe that this dispute must be remedied by the Congress and not by the Courts. They are relying on the Plenary Power of the Congress from Article I, Section 8, U.S. Constitution.
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.