"Train" 421 is actually two cars (sleeper and coach) that arrive from Chicago as part of the Texas Eagle #21. In San Antonio these two "through cars" are coupled to the rear of the Sunset Limited #1 to continue to Los Angeles. From San Antonio west 421 and 1 are actually one physical train so it doesn't matter which train you book. Check though as 421 may have a better fare than 1 (or vice versa) even though the both going the same place.

As for boarding, I've never boarded in San Antonio. I believe you have to wait (in the station) until near departure time to board the train. I've only been through San Antonio on the Sunset Limited or Texas Eagle and was allowed to remain onboard..I've been on Trains 1 and 2 NOL to CHI and trains 421 and 422 CHI to LAX.