I think you're assuming it somehow got attached
before the OP got to the exit gate, when in actuality it happened
after. Here's the theroretical timeline:
1. OP books with Chase UR portal. No way to add his EC# there, so no possible way it could be on there. All they have is the OP's name, email and maybe phone.
2. OP arrives at location and picks any car from the aisle corresponding to his status.
3. OP drives to gate and hands gate agent his driver's license. He either tells gate agent he's am Emerald Club member renting on a prepaid res, or National's system is smart enough to put one and one together when the gate agent scans his DL and auto-associate the res with his EC profile (yes, I'm aware that the likelihood of this is pretty small).
In short, the working theory is that you can have your cake and eat it too by booking a prepaid res without your EC credentials attached and have it done as you exit the lot--AND without stopping at the counter first. Someone here needs to test it, or I'll ask someone at AutoSlash to take one for the team to find out.