Some Superliners were set up with through MU lines to run in cab-car consists, but I don't know if Amtrak made this standard for them or not. When the San Diegans started "Custom Class", they used Superliner Coach-Baggages for this service on California Car equipment sets, and to provide a baggage space without a transition car. When the specifications for the Surfliners were drawn up, it was decided that the Custom Class cars had to have seating on the lower level - to meet demand and rectify complaints about providing the same level of service for elderly and handicapped.

Since each train had to have a cab car, it was decided to put the baggage section in the lower level of the cab car, which also reduced the number of passengers exposed in a collision. There was still plenty of lower level seating in the other two coaches.

I can't say what they did or are doing on the San Joaquins or Capitals. I believe the California Cars are still owned by California's DOT, so maybe they will reassign some of them.