If it makes the 9600gt out to be a better card on an Nvidia board, then they can use the marketing to contrast Nvidia "performance" vs. ATI's alleged second place status at that price point. The problem is that Nvidia's not being transparent about their behind the scenes overclocking of the PCIe bus, so people buying the cards for non-Nvidia boards might think their card performs better than ATI under stock conditions.
I find it interesting that the marketing and driver department are in the dark. While it could be marketed as a feature that recommends Nvidia boards, it comes across as just another behind the scenes Nvidia exploit that they don't want to be made public by their own team.
Intel should have bought Nvidia instead of developing their own GPU's, because the companies both operate with a questionable business ethic, even in generations where they have very competitive products.