My 40 minutes includes that calculation already. If you plan accordingly, you don't need to wait for the train... just arrive on time. I bike to the station so that I don't need to pay for parking at the station.

On a side note, BART is probably going on strike this week, which means that an hour BART commute is soon going to turn into a 4 hour commute when the traffic on the highways double.

Ironically, though that's correctly pointed out as a vulnerability of "public transit," it's also a vulnerability of private automotive transit: if not for public transit, it would be far, far less convenient to drive from point A to point B, at least for some values of A and B