Well;

"Same old stuff" wrote alot to say nothing.

If you are in Business class your ticket is reserved. If you buy a ticket to Chicago and don't show up for the first segment, say SD to LA they may sell your space on #4 to someone else, but I am not sure.

No chance to scan ? OP said O'side to L.A. a two hour segment.

On bad days the Amtrak crews go into the fetal position and hope your having a unscanned ticket will bring you back on a better day.

Also some crews check tickets at boarding and forgo seat checks. That helps keep the lost Metrolink/Metro passengers off train. That way they don't have to put them off at Commerce or Buena Park because of no fare (I have seen both). Some of crew likely was doing plan B on a plan A day.