The color choice is in the hands of fate now.
I decided that I wanted Electric Blue, but MINI USA told me that my car is in “Status 112 – Scheduled For Production” and they didn't think the order could be changed.
When I talked with Jeff at Hank Aaron MINI, he said it's possible that a change could be made, and offered to give it a shot. So we updated the order to Electric Blue with Silver wheels (everything else remains the same), and will just have to wait and see if the changes actually find their way into the production system.
The good news is that I was able to check out a Liquid Yellow MINI Cooper today, and I do like the color. It's not nearly as pale as I had feared, so if it gets painted Yellow, that'll be just fine too.