It's the difference between a census "combined statistical area" and "metropolitan statistical area". The CSA combines all the metro/micro statistical areas in a general area. See http://en.wikipedia.org/wiki/San_Jose-San_Francisco-Oakland,... .
http://en.wikipedia.org/wiki/List_of_Metropolitan_Statistica...
The wiki page suggests that these are based on social and employment connections that are inferred in part from commute patterns.
Perhaps the pairing of SF and San Mateo reflects growing social and economic links between the Peninsula and SF in a way that eclipses SF and San Mateo's historical affinities with Oakland and San Jose respectively.