I don't believe that the NOF process is enshrined in a Court Order. Even pre-Centennial Accords there were negotiations at PFMC and such. As I recall, NOF was developed to have a single, joint process.

It was NOAA that said they could issue separate permits but their "special relationship" with the Tribes would get a permit faster. The BIA action was probably not legal but nobody had the huevos to challenge it.