All (or most) of those are included in the COL estimates I've seen. Yes, the Bay Area is expensive. But, as best I can tell, the salaries (on average, per household) more than make up for it.

Trust me, I hear the same thing in discussions about DC area salaries and COL. Relative to the rest of the nation, software developers here have a high income and high COL, but the income more than makes up for it here too.