I haven't ridden Amtrak in CA, but I have on the East Coast (Wilmington - New York), so I will make two comments:

You can bring folding bikes on to any train any time. Amtrak insists they be folded (even with 10 people in a car that holds 80), but the folded bike will fit on the shelves for suitcases, or also in a larger space with no seats (for excess luggage, wheel chairs, etc.)

Talk to the people at the actual station - they can tell you what they really do. I've brought full sized bikes as checked baggage 2-3 times. The last time, the national information (800 Tel) told me it wasn't possible. When I went to the station, the baggage staff confirmed that of course the bicycle could be checked in one of their boxes. Bicycles as checked luggage will be useless for a daily commuter, but my point is that general Amtrak information is uninformed at best - check in person locally.