Quick note for poor souls like myself seeking to make a SoCal->NorCal biking trip:
So yes, you can place your bike in the in-train bike rack, as well as the cargo area of the bus (contrary to what Amtrak customer reps will tell you) without boxing it. There are some elements of uncertainty, however.
Option 1: Carrying the bike with you
2. Go to the Los Angeles Union Station, and print your ticket from one of the vending machines using your confirmation code.
3. Await the train in line with your bike.
4. When boarding starts, seek the car with the bike racks on them. During my OAK->SAC trip, the car was the last one. Can’t remember position of the LAX->OAK one.. I think it was about the third from the bottom.