I actually find the original palettes to be more pleasing than your reconstructed ones due to the hue shift. I can't help but go with what my eyes are telling me.
The original idea is that the ones on the left are uglier than the ones on the right because of their brightness. The rebuttal switches the brightness levels, which results in the same progression, from ugly to less ugly.
Sure, I only swapped the values and not also the chroma information. But the point was to refute the original article, not to set up my own controlled experiment.
As another example... if this hue shift was the main thing that mattered... well, I took his "ugly" combination and flipped the color information vertically, so now the hue shifts in the opposite direction from before. Does the new combination on the right really look better? http://www.hcs.harvard.edu/~jrus/ycnews/nonsense2.png