I know some of the PS stocks were "recovered" with only southern fisheries considered. I forget specifically which ones but is probably some of the southern PS stocks. They (NOAA) were also allowing total harvests on some PS stocks (Nisqually, Puyallup I think) where the recovery rate exceeded calculated MSY, as has been discussed here before.
Initially the Co-managers proposed exploitation rates for some populations that only considered Southern US (SUS) fisheries. (See the "Comprehensive Management Plan for Puget Sound Chinook, Harvest Management Component, written by Puget Sound Indian Tribes and WDFW.) Those populations included Mid-Hood Canal, Skokomish, Green R., and Lake Washington. There may have been others, but these definitely only considered SUS fisheries. Initially I believe that NOAA accepted the Co-managers' approach, but I'm pretty sure that there are now Recovery (or Rebuilding, depending whose terminology you use) exploitation rates that include all harvesters for every population.