I have ridden BART and Caltrain in the past for work. I've had commutes that involve transfers, too -- usually Caltrain to MUNI.
I don't think what you're saying contradicts anything that I said -- I said that the move to SSF makes it more difficult to commute via BART, but that it was too strong to say that it "eliminates" the possibility of doing so.
In any case, I really suspect that if companies keep moving to the SF Bay Area and keep growing, they're going to have to start moving to places that are out of the city. The rent per square foot in SF is approaching $85/ft^2, the highest it's been since the original dotcom boom; downtown San Jose is around $60/ft^2, better but not that much better. But places like San Ramon, Fremont, non-downtown San Jose, and yes, South San Francisco are around $30/ft^2. Some would argue that staying in the Bay Area at all is silly for tech companies at this point; while I don't think I'd make that argument, if I had several hundred employees to find space for, I just don't think I'd do it in the City.