I believe the author is missing some data sources (bus lines?). There are areas I know are reachable within 30 minutes from downtown Berkeley that do not appear on the map.
I used to visit San Francisco and the Bay Area a lot for work. I could be wrong, but it feels like capping the travel time at 45 minutes is too low. A lot of people down there seem to have commute times more like 1-3 hours each way. I assume the low cap is also why the map also doesn't include the Caltrain heavy rail line that connects San Francisco to cities as far south as Gilroy.