I don't think that they "ignore" it, in fact the plan acknowledges it by saying that additional fishery restrictions will not recover some of the populations.
However, that does not change the fact that the populations are in terrible shape and folks are proposing actions that decide what level of them can still be killed! See the rub? the answer should be NONE! But, since that is not realistic, given it would likely shut down untold numbers of fisheries that would otherwise be open, the alternative is not "Kill as many as you want", but rather, kill very few.
I know folks have a hard time with this concept. You can't just point over there at habitat and say "Hey, the problem is over there, not here!" while continuing to kill the fish at any rate that is not shown to be reasonably low enough to not drive the population past any reasonable threshold for recovery.
Back to something that Todd said a decade ago in this thread (my summary) - Either let these stocks continue to limit our fisheries or get to fixin' the habitat. Recently I heard the head of the Governor's Salmon Recovery Board talk about the cost of recovery. He stated that, to date, the actions called for in the Regional Recovery plans have only been funded by about 15%....