IMO, that's gotten way too complicated for a typical traveler. Most people don't want to deal with a city bus to the airport.Correct, which is the cheaper and often faster way to get to Diridon from the airport. Going by Caltrain you run the risk of hourly trains on the weekend.
The relatively easy way around that is to take the Rapid #522 bus downtown at the Santa Clara Caltrain station, which will stop within a couple-minute walk to Diridon. Not sure if it's faster than #60 to the light rail station to Diridon.