"Only" counts for something when you have to pay half of it to live in a reasonable location. That 90k in SF is around 50k in Hampton-Roads VA. That 90k in Oakland is around 60k.
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.
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.