2. To some, yes, because BART is getting crowded so many end up standing in a wall to wall claustrophobic space.
3. They are climbing higher, especially since Uber is moving to there, and they're only the vanguard. It's also been discussed as a cheaper alternative to SF for at least two or three years now.
I managed to make do with 50K a year, but I lived in San Jose and didn't have the expenses of car ownership.
Living in SJ required a 20 minute walk to CalTrain and then a 45 minute ride to the city by CalTrain (if I caught the express) and then another 15 minute walk to work.
Even though 90k is ~3x the average personal income for the US, when you're living in one of the most expensive cities in the country, you can absolutely be broke on that.
You can argue it effectively pushes down the size of the offers people get, but you don't have to worry about it when you calculate your net take home.
My point was that on $90k in SF proper, if you want a "nice" place, even a 1BR or studio you're going to be spending a huge percentage of your income on rent and basic necessities.