I am in security (but it's similar in many specialties) and while there are very good companies in Austin if I want to to rise become a security architect or director of information security I have to go to the tech headquarters. Companies like Google and facebook may have regional offices but the core innovative security/ai/pl work and executive decision making is being done in the home campuses.
That being said, I would never leave Austin for the SF bay unless it involved a $350k+ salary.
San Diego, for example, stomps all over Austin in terms of software jobs, and Austin's hardware scene is laughable.
Big ones: BAE, Northrop Grumman, and General Dynamics. (Previously I would have listed Qualcomm ...)
A zillion biotech startups: I drive past at least a dozen near here every day: https://www.google.com/maps/@32.9104712,-117.2304182,18.57z
Rockstar San Diego seems to be hiring as far as I can tell.
In addition, a lot of manufacturing companies up in the San Marcos/Vista area all need automation programmers.
If you're not finding SD companies with software jobs, I'm very surprised.