Thanks for the story from my side, too! Used to live not too far from there as a kid. Smelled the rendering plant when the wind was from the northeast (hot days). Remember vaguely tracks in the Crocker Industrial Park and crossing Bayshore. Wasn't there a spur into the PG&E substation at Geneva & Bayshore, too?
I do worry a bit about foundation conditions. It's basically unengineered fill on mud, worse the farther toward the main line (the Bay side) you go. The space between the tracks and the freeway was all garbage dump (and I do mean "dump" - no serious engineering or compaction in those days) in the 1950s and 60s, eventually covered with just enough dirt to build something light on. So if HSR wants to build a yard and shop in that area they definitely want to be on the west side where SP was.
Would a yard/shop there be HSR-only or HSR+Caltrain? With the city pushing for rerouting the line down through Mission Bay (in a tunnel, with sea level rising?) and eliminating the current 4th St. terminal yard, there won't be much space for daytime storage of commuter trains. Even the Transbay Terminal connection (unfunded, even by HSR) won't have local storage yard at the terminal. So Caltrain will need some place to park and service trains - I'm thinking Bayshore for them too? At least by then everything should be electric (except whatever freight service might remain) so the shops would be less of a local nuisance than they would be now (cue
story earlier in June of the locomotive fire at the Roseville shop that spread oily stuff around an adjacent neighborhood).