I had the “perfect” solution to the “lack of bike accommodations on Caltrain problem” about 20 years ago (shared in another Peninsula newspaper). It looks like it’s time to share it with the current generation of train-bikers.
After biking to the train station on a well-maintained, but unattractive bike, I parked (and locked) the bike and boarded the train. At the work-end of the train commute, I simply picked up a second, equally unattractive bike, patiently waiting to carry me to my work site.
Both bikes were very cheap, fully functional and in no way attractive to any self-respecting bike thief. It worked for me — I was never bumped for lack of bike accommodations, nor lost a bike in my years of bike-train commuting.