To answer your question, I don't know why NMFS chose this route. But I'm happy to share my opinion.
First, the 4(d) rule, as it's called was necessary to implement enforcement of the prior ESA listings. For the last year, only Federal agencies have been prohibited from jeopardizing endangered and threatened fish. Because of NMFS' regulations, only endangered fish are prohibiting from being taken from the effective date of a listing. Threatened fish can be legally taken (do you believe this?!)until the 4(d) rule against take is issued. So it's still legal to "take" threatened steelhead for another 60 days and salmon for another 6 months.
That's the main reason for this rule. It's required in order to give those ESA "threatened" species listings some backbone.
I'm not familiar with the exceptions that are included in NMFS new rule, but I think the intent is to enlist the aid of state and local governments. NMFS is not a very big government agceny; yet the salmon and steelhead listings issues are huge and pervasive across all walks of life. I think there's no way NMFS could ever enforce all the actions necessary to effectively protect salmon and steelhead habitat to the letter of the ESA. Much better to have the cooperation, even the unwilling cooperation, of the local jurisdictions that actually do issue permits to people on a routine basis to do ordinary things that degrade and destroy habitat. Only now there will be a catch. Probably not perfect - and that's why there will be no end of environmental lawsuits - but if county public works and building and transportation officials have to check off salmon protection every time they issue a permit or license, the amount of damage ordinarily done to fish should be significantly reduced.
I think Will Stelle recognizes that a perfect solution (everbody leave the NW?) isn't possible, so he's looking for a workable solution that allows a burgeoning population to coexist with salmon and steelhead populations that continue into the future.
That's kinda' simple and hardly qualifies as analysis. But hell, the experts probably haven't got it figured out, either. This really is complex.
Sincerely,
Salmo g.