Riding Caltrain during peak hours is totally fine and not unpleasant at all, particularly with the new trains (I do it most days and am writing this comment while doing so)
I left California before the new trains were a thing, but peak hours going north starting in Mountain View meant standing room only tightly packed on the world's more unstable train cars.
I took Caltrain regularly pre-pandemic when I had a job in Palo Alto and going to SF. It was not bad at all. Other cities like NYC had way more packed trains.
