The flight was super late (more than two hours), according to OP. The GAs did a great job in getting the plane out quickly once it was fixed. It would have been a disservice to the 100s of passengers at the gate (including that pax who was at the gate patiently wating for his upgrade to clear) to hold the plane endelessly waiting for the OP that decided to go to the lounge. In that hectic minute, when the GA is trying to get the plane out and after calling the OP's name, he was nowhere to be seen, the best assumption is that he was a no show. (The GAs can't keep track of every single person that asks them if it is ok to go to the boys room for a few minutes, lots of people do. GA had now way to guess that the pax missing was one of the ones asking if they had time to go away for x mins)

Also, OP says there was nobody at the gate, and the GA was walking out the bridge. This usually means that the flight was closed. In these circumstances, GAs will usually tell you that it is too late and try to rebook you on yet another flight. Actually, the GA went out of his/her way holding off the plane for a few seconds more to be able to accomodate OP.

Later, the OP got the miles difference refunded.

I think the OP got outstanding customer service, actually.