It does confuse some agents - when I went to Vegas for my anniversary, I booked myself a revenue ticket (for DEQM) and then a reward ticket. I flipped off the upgrade so we could sit together - but the computer ran EUA anyway and I had to call to get back into Y. At the airport, the agent saw I hadn't been put on the upgrade list and offered to add me, and I told her it was so we could sit together. She said, "Oh, but I could add him too!"

I pointed out that he was on a reward, and she didn't think that would be a problem - until her supervisor came over and assured us that it would.

But this was the same agent and supervisor that gave a non-elite a free day-of-departure upgrade, so clearly they know how to override or side-step some rules. :P