A couple things to unpack here:
1. This isn't about the gate agent at all. Just like passengers can't make duplicate bookings, there are automated systems in place at AA to track employee duplicate bookings. I assure you it's not a manual process.
2. How do you expect he's going to board with both seats (assuming SABRE/QIK even let him check in with a duplicate reservation)? Is he going to show both boarding passes to the gate agent?
3. Gate agents aren't responsible for this kind of discipline, and at the end of the day AA doesn't really care about the D3. What they will do, however, is discipline the employee whose benefits the D3 are abusing, which is the point many of us are trying to make here.