Yes, Bay Area rappers do sell hundreds of thousands of records independently, BUT it happens over the course of their entire career rather than the span of a few weeks or months like mainstream rappers.
The difference is that independent rapper see every penny of every dollar they make. Rappers signed to majors only make a few cents off of each album they sell.
Add to that, taxes, promotion, high cost of high-profile celebrity rapper/producer features, 360 deals, hefty child support payments and good ol' fashion trickin all add up to eat up mainstream rapper's pockets.
http://www.refinedhype.com/hyped/entry/chief-keef-average-orthodontist
But back to the Bay Area. The Bay is one of the only places in the world where an artist can be huge locally but completely unknown nationally. People from the Bay support their own artists more than anywhere in the country. Although cities like Kansas city also keep Bay Area rappers alive and well-fed:
http://spingineer.wordpress.com/2008/12/06/history-of-pre-hyphy-and-non-hyphy-bay-area-hip-hop/
The Jacka, who was the number one selling rapper from the Bay at one point in time, easily has sold over 350K in his career. He has sold over 500K independently.

And much of his support came from outside the Bay. About 60% of the Jack's sales came from outside Cali:
http://en.wikipedia.org/wiki/The_Jacka
http://www.100grandonmywrist.com/2012/01/jackas-verdict-song-by-song.html
My old neighborhood alone has birthed such local sensations. Even some of the little known underground rappers in the Bay have sold 250K independently over the course of their careers. Case in point, Willie Henn from Fillmoe in San Francisco. Check the end of the video where it says he sold 250K units independently.

http://www.youtube.com/watch?v=Z2SXqdxL0-0
At the end of the day, successful Bay Area rappers known how to hustle. They prove that Youtube views and being on MTV Jams don't mean sh!t and that you don't have to be a household name with lil crackas like Justin Beiber to make money.

And from what I've seen, independent Bay rappers are more likely to invest they money into lucrative non-Rap ventures instead of tricking it off.