In response to my previous post, I received the following email from Greg Fischer. It contains such a wealth of information, I didn’t want it to be obscured as a comment. For lots of great information, check out Greg's terrific blog. And I enthusiastically second his praise for the Amtrak reservations people (1-800-USA-RAIL). I have always found the agents friendly, competent and happy to rummage through all these complexities to come up with the lowest fare.
The rail fare portion of your trip from San Antonio (SAS) to Los Angeles (LAX) should never be anything other than $138 when you are booking a sleeper.
When occupying a sleeper accommodation, Amtrak always assesses the lowest rail (coach) fare, regardless of whether the fare would be available if you were only buying a coach ticket.
The lowest coach rail fare from SAS to LAX is $138 (before discounts such as senior, AAA, etc.) and the fare basis code is DOF1. It makes no difference whether it is on train 1 (Sunset) or train 21/421 (Texas Eagle).
The accommodation charge for rooms is a different thing. Amtrak has 5 different levels, which like airline seats (or Amtrak's coach seats), are yield-managed.The five different rates for the roomette (formerly called economy bedroom) between SAS and LAX are as follows from low to high: ED - $149, EC - $224, EB - $299, EA - $273, ES - $448. So depending on the availability of roomette inventory, the add-on ranging from $149 up to $448 would be added to $138.
Since functionally, trains 21/421 and 1 operate as a single train between SAS and LAX it really doesn't make much difference which one you booked.Rather than use Amtrak.com, you might just call Amtrak's call-center since unlike most airlines, they do not charge a fee for working with a reservations agent.
You may find a blog series I'm writing useful in understanding how Amtrak fares work. I'm in the process of writing the chapter about fares for sleeping accommodations.