First, I can't speak to the 3 hook problem because I don't live in Southern Cal. However, I believe only one PSL (Pacific Surfliner) has a baggage car; and I believe for that reason, the bike policy is somewhat different than the other PSL's.
As far as the baggage car is concerned, IF the station has baggage service, then bicycles can be checked in a BOX for $5. You can use your own box or purchase a huge one from Amtrak for $15. However, I think the gotcha here is that baggage must be checked 30 minutes prior to departure. There are good reasons for this, some obvious and others not so obvious.
It is the station personnel who handles the checked baggage, including bikes. The conductor or assistant conductor will unlock the baggage car; but would never take baggage from a customer on the platform and put it in the baggage car, never has and unlikely ever will, again for good reasons, most not obvious. There has been no company change to implement an anti-bike policy. Of course, it would be nice if Amtrak was like European railroads regarding bikes (and a lot of other things). But Amtrak operates under severe political and financial limitations. Did you know that all baggage cars are over 60 years old; and they have a lot of trouble keeping them on the rails?
I can sympathize with the frustration of not being able to just appear on the platform with your bike, because that would be a nice service. However, a little planning and knowledge could have avoided problems like this. As several people have mentioned, the bike policy is actually pretty clear. It along with which trains have baggage cars and which stations have baggage service can all be found on the website.
The above being said, not all Amtrak personnel know and follow the published policy, bikes or otherwise, for two reasons: 1) lack of training or poor communication, and 2) laziness. If you know the rules; and a conductor, assistant conductor, or service staff (e.g., snack bar attendant) violates it and it causes a non-trivial problem, contact Amtrak CUSTOMER RELATIONS (call 1-800-USA_RAIL and ask for them). The first thing they will ask you is did you get the employee's name. If the problem was serious and you persist, they might even give you a voucher for free future travel. Of course, it you are really PO'd, this will be worthless. But give it a chance and your experience may be exactly the opposite the next time.
Having travelled over 110,000 miles on Amtrak, almost always with a bike, my experience has been, that for every employee who breaks the rules in their favor (to save them work, perhaps), several others will break them in your favor. For example, not long ago I saw a couple unload a tandem at Cumberland, MD, from a coach. Very much against the rules. When I recently boarded a Missouri Service train with a bicycle without the required reservation and ticket, the conductor sold me one anyway. He also had me put it in the overhead rack, very much agains the rules.
In the past several years, Amtrak's Downeaster has operated from Boston, MA to Portland ME, making stops at many towns along the way. Bicyclists can easily roll their bikes onto the train with then and place them in specific areas where there is extra space. But this only works for bicyclists who are traveling from Boston and Portland. This isn't allowed at the other stations the train stops at. How inconvienient.