Earlier quoted context omitted.
To be honest, a train leaving early SUCKS. You show up on time, and you find out you missed it. Maybe the next one is in 40 minutes, maybe it's the next day. (I realize 20 seconds early isn't that bad, but still, leaving early by any amount of time is a lot worse than leaving late)
In this case, it's annoying because you'll have missed a semi-rapid and the next comparable train to Tsukuba will leave 9 minutes later and arrive 17 minutes later. It's not a 40 minute thing, this isn't Caltrain, but it's still annoying.
Why don't they just build out BART between Millbrae and Santa Clara? Once the Silicon Valley Extension is finished, BART will be almost a loop around the Bay except for that gap.