That is, the salary to expenses ratio isn't the only thing to look at.
For example, if you save 10% of your money in SF and make $150K, that's $15K a year in savings. If you save 14% of your money in Austin and make $100K, that's $14K a year in savings.
Even though you went through 90% of your salary in SF and only 86% in Austin, living in SF is better, because you saved more money in absolute terms. You can move elsewhere and take advantage of that savings.
If you only care about money, the ideal strategy is probably to move to SF in your 20's, make a high salary, and then move out of SF. A lot of people these days don't have kids until their 30's. (Anecdotally that seems to be what a lot of people have done in the past decade -- move out of the Bay Area when they want to have kids.)
This also doesn't account for the fact that SF has more "outliers" and more choices. You might be pleasantly surprised by the kind of job you can get or the kind of money you can make in SF. In most cities (certainly not all), you probably won't be surprised. The job market is what it is.
(I'm assuming something about their methodology here, feel free to correct me if I'm wrong.)