While the agent today can technically pretty much give that upgrade to anyone he wants, he was wrong and surely he knew it. The list is the list. He can tell your "stinkeye" passenger's companion was further down the list. At the gate, they are absolutely supposed to go by said list.

Consensus seems to be gate process will remain the same after UDUs at the gate. UDU just reflects a change in instruments for early confirmation. Of course since every MP member will be added to the list by default, lists will get a bit long in some locations