While it may be correct that "folks who want to make a lifestyle choice of going to Austin from California should get paid less to do it," that is not what this article is about. Instead, the author is talking about Austin companies trying to bring developers there that otherwise would be somewhere else (i.e. people who do not want to live in Austin). In that case, its a simple matter of value to the potential employee as to how much extra they need to be paid in order to relocate to somewhere that they had no intentions of living.
Agreed. If you're a developer looking to live in Austin, you may very well expect a lower salary; but, if someone is trying to recruit me to Austin, I'd actually expect a higher salary than in California, as I would much prefer San Francisco to Austin. (Quality of life considerations might come into it as well, as mentioned in the article; $150k will get you much farther in Austin than in San Francisco. But I only spend so much of my money locally; don't expect me to take a paycut to come out to live somewhere I have no particular interest in living.)
edit: repeating myself