The most important factor in their BS Score is transmission, which is why the cheap 50/1.8 lenses from both Canon and Nikon score several points higher than any of these 500/4 lenses. It's only when you have lenses of identical max aperture that the other stuff has any influence. BTW, while the 500/4s score 25, the Canon 50/1.8 on a 5DIII gets 28, and the Nikon 50/1.8 on a D800 gets a 31, and main measurement difference between the 50/1.8s is that the Nikon is 1 P-Mpix sharper (put it on the D3X, it's sharpness and Score tie the Canon). So, the Nikon 50/1.8 is 1 P-Mpix sharper and gets a Score 3 points higher, the Canon 500/4 is 3 P-Mpix sharper, but the Scores are equal.
I begin to wonder if the 'secret metric' you mention is sponsorship...
If transmission really was the most important factor then the Sony should be out scoring the Nikon. The Sony equals or beats the Nikon in all the listed categories and has the lowest transmission of the three lenses.
Basically I think DxO are a bunch of Nikon fanboys. The individual ratings are fine, but the composite scores ae just ridiculous.