The article is comparing median income (of all residents) to prices that home-owners pay which is pretty much apples to oranges.
Fewer people are buying houses in the Bay Area right now already which causes the disparity in the house-price-to-income ratio: Most folks who can afford a house worth 1M (and prove it to a lender) are probably earning dual-income in the tech sector and 330K (which would make the ratio 3x, same as the national average) is not too much of a stretch between two technology jobs.
Fewer people are buying houses in the Bay Area right now already which causes the disparity in the house-price-to-income ratio: Most folks who can afford a house worth 1M (and prove it to a lender) are probably earning dual-income in the tech sector and 330K (which would make the ratio 3x, same as the national average) is not too much of a stretch between two technology jobs.