You say it's cheaper, then use the example of a $2000 apartment which is an
insane amount to pay for housing. Then you (correctly) note that the cheap places are actually really far (and annoying) commutes. BART stations are much cleaner than NYC subway stations, I find the trips much more pleasant.
Your startup could also be in SF (not MV) saving you the commute, have you thought about that?
Eating fast food Good, healthy, cheap food in SF is pretty common, it's the lifestyle there.
> Door to door will typically take him ~35 minutes.
Bull. Maybe if he jumps out of his building, sprints to the stop, and the subway car just happens to be waiting for him the moment you get there. The fact is that if you work late into the night, the cars come less frequently, especially to/from places outside of Manhattan. You have to factor in average wait time (since NY Subways still don't track subway cars like any other good transit system). My closest subway stops would also be closed for days or weeks at a time randomly for upkeep. Don't forget that, during rush hour, you stand in a sardine can with a hundred other people.
Also, NY culture is a consumption culture. Even if you can possibly scrape by with less, you're in a culture that actively goes out and pays huge amounts for drinks at bars, measures class by where you live and places you shop, and you'll invariable end up paying some or a lot of money for cabs because of closed subway routes or maybe you just get sick of the dirty, cold subway.
I've done startups in both areas for years. I notice that people in New York justify the low quality of life by claiming the best possible aspect of something is the norm. It's not the norm. 35 minute commutes from Brooklyn, $2-$6 appetizers (who measures food costs in terms of appetizers??). $1000/mo one-bedrooms and 7-minute commutes have 0 correlation in NY.