The site speculates NVIDIA initially allowed the GeForce GTX 680 Classified because it would serve as a good marketing tool to set overclocking records, but forced EVGA to cripple the card once it had served its purpose. Officially, the program is designed to smoothen the launch of new GPUs and to reduce RMAs, but NVIDIA's add-in board partners aren't happy because Green Light puts too many limits on how they can differentiate their graphics cards.
Some parameters of the Green Light program are that vendors have to send in their board designs for approval from Nvidia to meet Nvidia's noise, power, voltage and heat figures. If those figures are not met, Nvidia does not approve the card. If a company does not follow the Green Light program, they risk losing their GPU warranty and BIOS support. More importantly, they could possibly risk their allocation according to some AIBs.
In addition to the design of the card itself and the aforementioned parameters, Nvidia also restricts certain software from being bundled with the cards by the vendors. One example was when MSI released the unlocked BIOS with high voltage in their Afterburner overclocking utility. Needless to say, Nvidia was not happy and forced MSI to immediately remove the feature