They are running multiple trains. SF to LA non-stop trains won't even stop at stations like Gilroy or Madeira. The all-stop trains will preference commute hours. The seats are non-rivalrous: Central Valley commuters aren't even going to be on the same train as a SF to LA business traveler. It seems reasonable that fares would differ, and that traveling just 1-2 stops from SJ to the Central Valley will be a lot cheaper than going from SF to LA.
This really depends on how it ends up being priced.
In Germany, you can pay for a year-long high-speed rail all-you-can-ride pass. It costs just under 5000 Euros, which is very reasonable if you're using it every workday.
This is a bit like AWS pricing. If you book an entire year of usage up-front, you get a much lower price. Casual users pay much more per use.
OTOH had altamont been selected, it would have been extremely useful for commuting from sacramento to the bay (branch line, no seats to displace)