PDX, your answer was about what I was expecting. In general, these three locations do seem to be hemmed in close to the coast by mountains, with no easy link to the rest of the U.S. that doesn't involve steep, twisting grades.

Except, that is, for San Diego, which of course has good rail access in and out to the north. Considering the grades which trains already face on Cajon and Beaumont, the 2.2 percent over Miramar Hill should be of no greater consequence to new intermodal business (and has long been used for occasional bulk export traffic) should the port(s) of San Diego go big-time. However, the gauntlet of passenger trains that swarm the Surf Line might limit much of that new freight traffic to night. Not to mention the roundabout nature of moving such traffic north along the coast, east through the Santa Ana River canyon, and back southeast toward Yuma if it happens to be destined for markets in the southern U.S.

East of San Diego, the Carrizo Gorge Railway has been quietly upgrading the former SD&AE in recent years. The work needed to completely turn it into a viable east-west port corridor would be a small fraction of what will have to be done to engineer a new railroad over the mountains of the Baja Peninsula to Punta Colonet. And the grades on the CGR are no worse than what would be necessary to cross the two ranges east of Punta Colonet. Only other option is to approach there along the coast from the north, which looks challenging to say the least with cliffs rising right out of the sea.