FNP,
The best available science was presented to the administration. This science doesn't meet the administration's policy needs. Consequently, the administration is/has developing/developed its own science/ ESA interpretation, and is issuing a policy consistent with its needs.
A suitable anology may be found in Weird Science, the website that described the ANWR study of 200 some pages over 2 years that described the threats of oil drilling in ANWR to wildlife. That study was at odds with the administration's needs, so Secretary Norton found (apparently, never figured out who they are) two USGS scientists, who in 2 weeks produced a 2 page report that oil drilling wouldn't harm wildlife. That was declared the best available science, at least the best available science that supported the administration's policy. I believe we can expect more of the same on behalf of the new salmon policy.
Fortunately for salmon, the administrative record is very strong with respect to ESA listings generally, and the distinctions between hatchery and wild salmon. The environmental groups will likely use the Freedom of Information Act to obtain the best available science when they sue the government, which the courts will probably find doesn't support the the administration's policy. But the election will be over by then.
Sincerely,
Salmo g.