I liked the system colored nub as well, but it would only really work for Nintendo if they were only going to release one color system. It would be too expensive otherwise, and the system is presumably quite expensive enough.
Also, a cover for the nub might prevent the 3DS from closing properly as there doesn't seem to be much extra space on the system.
That video wasn't up when I first saw the article, and it was presumably stolen before the firmware was uploaded, which might explain why it didn't turn on according to Engadget.