Plenty of people -- most people? -- in SF have a car too, and no, you don't actually need $500/month for a car. And hey, it's eminently possible to live in Oakland without a car if you really feel that's a priority.
I agree with you: the market is efficient. It's efficient and filled with people who put a big premium on being near the hip areas of SF. If you have less money than those people, you can get more monetarily efficient by being willing to be farther from the hip areas of SF. If you have identical preferences to a bunch of other people making $100,000-$150,000 in an area averse to adding housing density, then... well, you're going to be bidding a lot for a limited supply of housing.
My point is that if a company wants you to work in SF, you should be demanding a salary commensurate with the costs of that lifestyle. Making an excuse for the company not to pay you is silly. Making a daily BART commute and living in Oakland is fine, if that's what you want to do, but you shouldn't be doing it because a tech startup won't pay you enough to afford housing near where you work.
It would help if more than ~20 blocks of San Francisco were conveniently accessible by subway. BART, MUNI, and Caltrain are woefully inadequate.
Add in the cost of a car (which you need if you're living over there) and a daily BART commute, and you've easily added on $500-$1000 a month in transportation expenses. Again, housing around here is an efficient market, modulo the cost of commuting.