I mean, my earlier analysis (another thread) just used the compensation figures from the fine article. Maybe those figures are an inaccurate comparisons of the two cities. If we can find a better data source, I'd be happy to re-run with those numbers. Ditto on the housing cost numbers.
It's certainly possible that one could put aside slightly more money in SF than Austin off a much bigger comp package for the same role.
Anyway, Google and Facebook are just two employers. Clearly the average junior compensation is somewhere lower. I made a lot less than that as a junior employee, but it was a few years ago, not in SF, and not for Google or Facebook.
As far as Seattle goes, I think that the state tax makes up for most of the comp differences, and housing is cheaper there, so its a better value if that's all you're optimizing for.
That said, those jobs at $bigCo also make up a smaller portion of the job market in every other city. In the bay area, something like 1% of everyone (not just SWEs) works as a SWE at Google, Facebook, or a similarly paying company. Seattle is similar, although with Microsoft and Amazon instead. While there are some jobs that pay six figures in Atlanta or Austin, they're fewer and further between.
As a result of this, I know lots of people who make 150K+ all in comp in the bay area and Seattle, and no one who breaks 6 figures in, say, Austin (all at a Junior/New Grad level).