I can do no more than guess, but I think you are right about the San Francisco district. It is a large district and the notes have to be physically carted back and forth to some distribution center, so it looks like they created three locations to do this - one in San Francisco, one in Seattle, and one in Salt Lake City.

I'd also wager that the relatively small discrepancies in the borders are due to the federal reserve being practical and slightly shifting the borders to be cost effective in transportation costs, to deal with one district having an excess of supply and a neighbor having an excess of demand, and so on. When I look at a lot of faint borders near each other on this map, it tells me that this is border movement caused by these kind of federal reserve actions.

The one thing that is blatantly obvious is that the author clearly did not find natural borders of economic activity as he or she claimed.