That information would have been known to the gate agent(s) as jumpseaters would have required a cockpit pass or nonrevenue ticket.
This is true. I have had millions of those little "used" stubs in the last 10 years. If there was a pilot on the jumpseat, then AA knows who it was. Also, unless they've changed their policy, AA pilots would only ride in the cockpit if the cabin was full.
It would be unusual at least for an AA pilot to be sitting in the front when all of those First and Business class seats were available, especially on a long flight!