It's verified beyond doubt your fare basis is discount consolidator.

It's certainly possible for the discount consolidator fare basis to cost more than what you originally paid, so that's not unreasonable. Your original ticket wouldn't allow changable dates, but the upgraded fare did, so the extra fee made sense.

The only question is whether UK AA normally sells discount consolidator fare basis fares. Could be? Doesn't happen in the USA, maybe it does there? Once you contacted UK res office to rebook and change your fare, you were no longer dealing with a pure AA.com fare. So you can't complain that an AA.com fare didn't get you miles, when you yourself asked to change it outside of AA.com reservations. The only remaining question is whether UK res was right to sell you a non miles earning ticket. Not sure.