I find it interesting to see the variety of responses you have to this thread. I attribute this to four factors:

1. The guidelines you pointed at are a good starting point for Amtrak-wide guidelines covering general trains with hooks or as checked baggage.
2. Individual trains will vary in how they are outfitted for bicycles.
3. San Diego has multiple connections into the Amtrak network as well as local commuter train.
4. Local conditions such as track reconstruction or extended outages can also change things.

My experience with San Diego is dated (2009 last time I arrived by train). At that time, there were three general connections: (a) the Pacific Surfliner went up the coast to Santa Barbara or so. It seemed to have bikes go in the passenger compartments (b) the Coast Starlight stopped in Los Angeles but you could connect via Surfliner in San Diego (c) I believe there was commuter rail in San Diego County.

In my 2009 case, I was coming from further north (Portland) and boxed my bike in both PDX and San Diego and it transferred along with myself in LA. That was 13 years ago and since then I don't know how Coast Starlight has updated (e.g. with hooks in baggage car similar to Amtrak Cascades and Sunset Limited?).

Still think it might be helpful to check on notes for local outages and also understand which train services your route and what mechanisms it has available for bikes since that gives clues on what choices are possible.

Update: Also remembered, I traveled from San Diego to Portland on Amtrak in October 2016. On that trip I boxed my bike in San Diego.