Of course, the big difference is that Stripe's current office is at the edge of SOMA and Mission Bay, within pretty short distance of the Embarcadero and Financial District. Their new office will be...a business park. No offense to business parks -- Bishop Ranch in San Ramon is unexpectedly lovely -- but they're rarely known for their vibrant cafés, restaurants and nightlife.
You're going from a local commute to bart -> walking to the office, to a local commute to bart -> going to a station that is skipped by 3/4 of bart lines (ie requires an xfer for Antioch, Pleasanton, or Fremont) -> a shitty bus. NB: Bart is ass and generally is too incompetent to align train and bus schedules.
This adds probably at least 45 minutes each way for anyone coming from SF or East Bay locations and using public transit. It's an enormous downgrade.
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.
How do you think most East Bay commuters are getting to San Francisco?