It probably has more to do with the gate agent and the required paperwork. Once the flight is "closed" the captain gets a final report with # of pax, cargo load, etc., and the GA turns this over to him.
If they were to let you on board it would have to be redone....how much work is involved I don't know.
It is a valid concern I think though that they are closing the flight 15 mins before scheduled departure...just too early especially in your case when you have a tight connection. They still exist despite AA's efforts to reduce them.
GA has the final word on this, at least at the airport. Not sure what AA would have to say about it if you wrote them...