There are three ports in So Cal large enough for container yards: LA, Long Beach and (possibly) San Diego. Of the three, San Diego is by far the best choice for combining naval/(possible) commercial shipping/container traffic with a downtown Santa Fe station as it pretty much does just that IRL.
Looking out to the west, the far distant horizon at both LA and Long Beach is what you see, regardless of viewing height. Which begs the question: What is the viewing height for a typical yard viewer/operator here? Standing? Sitting? Closer to ground level the better, IMO, so you avoid looking "down" at a distant horizon as much as possible.
San Diego is quite different: Looking west out and over the top of said yard or station, you view the eastern side of Point Loma which looms ABOVE what would otherwise be the same ocean horizon viewed at many other ports...and even though North Island NAS fills up the middle of the harbor, the wall of Point Loma still seems close (to my eye, anyway).
Further south, along the Silver Strand, the far horizon opens up to a the normal flat line, which is fine...but the SD-SF-now Amtrak depot is downtown, and inside the arm of Point Loma--perfect, IMO.
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FWIW, and as to why I wax so enthusiastic about San Diego: It's the western terminus for my own railroad "scheme," right down to the palm trees.
A natural for me, as my paternal grandfather was chief dispatcher there (for the Santa Fe), right through the end of WWII--he died in 1947.
As it happens, mom's two oldest sisters ran the Railway Express Agency station atop the small "pass"--I might almost call it "Miramar Pass"-- where the Coastline heads north out of the city. There was then and still is now a wye atop the pass, and I THINK (but am still not sure) that small REA agency/station sat inside the wye itself. A busy place during the war, as the Marine Corps staging base at Camp Elliott* was the terminus for the leg that ran east off that wye. AFAIK, almost every Marine who fought in the Pacific, from Guadalcanal, right through Iwo Jima and beyond originally staged at Camp Elliot before shipping out.
[*Some of the old foundations at Elliott might be here:
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As far as the wye, you can see it on Google earth NNE of the city. It seems to be home to a "dead boat yard" today. Pretty sure I can see the remains of both the SS Minnow and PT 73 just laying about....
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Love your work, beiland.