The BIA is not a fishery management agency; it's a federal agency charged with fulfilling the various trust responsibilities of the federal government to Indian tribes. Under the 4(d) limit rule (as best I can figure at this time), a party can apply for incidental take coverage of ESA-listed species while undertaking an otherwise lawful activity. Since the BIA is a federal agency, it has a "federal nexus" and can apply under the rule for Section 7 consultation with NMFS. Section 7 is more straight forward and usually quicker than Section 10, which is used by non-federal entities. (I think this is why it's been said the tribes can get an approval faster than WDFW, which is non-federal and has to use Section 10.)
Although BIA is not a fishery manager, it works for tribal governments who are fishery mangers, or co-managers with the state. The existing PS Chinook management plan was first submitted by the BIA on behalf of the PS tribes, and WDFW rode the coat tails of that plan for the convenience of getting in on the easier Section 7 consultation.
About federal hierarchy: In the president's cabinet there are several Secretaries. Under Dep't. of Commerce there is NOAA, which includes the nat'l. weather service, nat'l. ocean service, and nat'l. marine fisheries service, or NMFS. The Deparment of Interior includes the BIA, along with nat'l. park service, BOR (Reclamation), BLM (land management), USGS, USFWS, etc.
So BIA is the federal nexus and figurehead submitting a Fishery Management and Evaluation Plan (FMEP) to NMFS under Section 7 of the ESA. After NMFS reviews the plan for sufficiency and offers it to public and technical review and comment, if found OK, then NMFS writes a letter of approval to the federal action agency, the BIA in this case, and the plan and the fisheries it covers are good to go.
The statements that NMFS sees the Swinomish spring Chinook fishery in the Skagit as OK, or has given preliminary approval is total horse pucky. (And let me add, I have no personal problem with this fishery. It is consistent with what the Tribe has been doing in recent years, except for having an approved plan for 2016. Further, I have friends and acquaintances in the Swinomish Tribe.) However, there is no such thing as a verbal approval nor preliminary approval of an FMEP at law. At law, there is a written letter or there is nothing. Just like the salmon and steelhead hatcheries, there is a NMFS approved HGMP, or there is nothing.
Oh, and a letter from the BIA approving the Swinomish fishery equals nothing at law under the ESA. If such a letter exists, it is meaningless at law if brought into court.