Gate agents (at any station) can't upgrade people - they walk around the lounge and process various gates or work at reception. A load controller who is somewhere not at the gate/lounge has absolute control over (along with the Captain, of course, jointly) who and what gets on that plane, and where someone sits. What happens when you get an op-up at the gate is that when your boarding pass is scanned at the gate, the system recognises a discrepancy between what your printed boarding pass states is your seat and the actual seat in the system. You are then issued a new boarding pass and the old one thrown away - this way your new boarding pass matches the manifest. The gate agent has nothing to do with this process - the new assignment has already been made by the controller (who might be at the gate, but he/she will 99% of the time not be scanning pax boarding passes at the gate, they have much more important things to be doing).

Similarly with your situation with the op-up at the lounge entrance. The lounge entrance agent has absolutely no authority to upgrade you - he/she can move your seat around the cabin, unless the load controller has locked it and all assignments must go through them - either the agent has got on the phone to the controller giving him/her your sequence number who then confirms your seat location (this happens when an agent can't "find" you in the seat stated on your bp, or the upgrade has already been processed before you even reach the lounge and so there is a discrepancy between your stated seat and the seat displayed in the system, which necessitates a new boarding pass being printed for you.