It seems to me that one of the bedrocks of Democratic victories in Presidential (and other state wide races as well) is that the San Francisco Bay Area is Democratic both in its urban core, and wealthier suburban outer areas. In most American urban areas we find a liberal urban core, such as Detroit, Chicago, St Louis, Houston whatever, but this heavily Democratic area is usually at least partially neutralized by a conservative suburban area so the overall vote count isn't so strongly Democratic.
In the Bay Area, this neutralization effect is not in play, as the wealthier suburaban counties of San Mateo, Marin, Santa Clara and Contra Costa still lean Democratic to varying degrees, so the overall effect is a massive surge to the Democrats from the entire Bay Area. I'm wondering if anyone has done a study called "if Bay Area counties voted like other similar counties elsewhere in the country". My guess is that California would go from sure Democratic state to leans Democratic.
You are right that it would be much more likely that California would be lean dem if the bay area voted "normally". This is especially true when republicans are able to do well with latino voters and can win the central valley and suburban LA by large margins. This happened in 2004 but strong performance by Kerry in the bay area assured he would win the state. I have noticed the LA area votes about the same as the rest of the state, and it voted about 54-44 in 04. If the bay area voted like that I think Kerry would have only won with a 5-6 points instead of the double digit victory he enjoyed(estimate). It wouldn't have mattered much this year as the real swing for Obama came in Southern California.