I asked a conductor on the Amtrak Pacific Surfliner what they do with bikes (assuming there is a bike reservation in place), and he wasn't sure. All he could tell me was they go somewhere else in the train.

Anyone know? How safe are the bikes?

I was in the business class car, I'm not sure if the conductor was new, only works that car, or what. From my perspective, I would prefer to park myself in close proximity to the bike.