Madison was a federalist. I suspect had I been around then I'd have been an ardent anti-federalist so this I'm ok if I occasionally end up on the other side of an issue.
Unfortunately, there is nothing that can be found (that I know of) in the records that pertains to why Madison took that action.
All we know is that he took that action and removed the definition.
By the way, one of the theories of Gordon was that Madison may have wanted to give the States more rights when it came to citizens - so he took out the definition.
Seems to me that the natural born citizen definition should be the same for every State ..so I don’t quite understand that theory. I must be missing something in his analysis.