I have used the California Surfliner for bike transportation prior to the tour on two ocassions..
THere are special hooks at the end of the car for bikes..You can ride with the bikes as long as you get the seat you need first come first serve.
One problem I found with the Surfliner...The entrance area to all cars have hooks for hanging bikes...You get on late in the trains schedule, passengers load the bike storage area with personal luggage. It will get loaded with bags, leaving no room for your bikes.. These storage areas. I am pretty sure there would not be enough room for a Yak...
Some of the older trains have not yet added the storage areas for bikes..In this case, you have to put your bike in the baggage car...Once I had to do that...So I locked my bike to a post and felt pretty at ease over the bikes safety...Should you be alone with the bike in the open storage area, it will be accessible to all, should you walk away from your club car.( again, the newer cars.)
If all went well, it was a great arrangement...No charge either.