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.

https://hsr.ca.gov/wp-content/uploads/2024/02/2024-BP-Servic...