Hmm. I actually had a slightly different experience. Admittedly, I didn't actually make it to the gate agent with a car from the aisle, so can't comment on if that works or not.
I recently rented from JFK with a reservation for a midsize booked through Chase UR. Got to the aisle, and the manager, who was hanging around, asked me what I had booked. I told him a midsize through Chase UR.
He said that I needed to go to the counter to fill out a contract. I told him I was an EE, and should be able to add my EC# directly at the gate. He said he didn't think so, and he called up some other manager who agreed with him.
So I went back to the counter, he printed out the contract, I signed, and then he says - you know, because you booked through a 3rd party, you can't pick from the aisle.
I showed him a conversation I had with the National twitter rep, who said that adding my EC# at the location is fine - but he was adamant. (At this point, I didn't think showing him the flyertalk thread would have helped any more
)
Eventually, after seeing how much luggage I had, he was willing to let me "upgrade" to an SUV at no added cost... So all's well that ends well.
