This says the price of mousing in SF has only increased by 78% since 2000. I spot-checked that, and the first alternate source of data I could find, https://www.paragon-re.com/trend/san-francisco-home-prices-m... , says the increase has been much larger.
It looks like the Paragon data is nominal dollars but the Economist adjusted to account for inflation. If you flip the Economist chart to nominal dollars, it's a +158% difference, so that's a good chunk of the difference but not all.
It is unclear which definition of "San Francisco" they are using. Is it just the city of San Francisco, the San Francisco-Oakland-Hayward, CA Metropolitan Statistical Area, or the San Jose–San Francisco–Oakland, CA Combined Statistical Area? I would guess that since San Jose is not listed separately, they are using the CSA, which includes a lot of outlying areas.