I mean, "Best City" as described by the article is a really loaded term because it means a bunch of different things to different people. Some people like to optimize for net income. Others might want to optimize for like-minded folks, support networks, and peer collaboration. Still others might want more health oriented amenities and pleasant weather. I think you're right though; by excluding these software engineer-dense cities, I think the article is missing the point of what might be the "best city" for a software engineer. After all, if they aren't even in the top 10, why are people even there? :)
Anecdote: at my current job in Houston, I know I earn a significant amount more than my counterpart in Austin, and I get a way less cost of living also. I also know that Austin has way more opportunities than Houston does, so I'm screwed if I ever want to leave this job. My personal situation matches the chart in the article.
I think this list would look a lot different if the jobs it considered were scoped down to software companies, and excluded the line-of-business development jobs that characterize most of the openings on cities outside the big tech centers.
Anecdote: at my current job in Houston, I know I earn a significant amount more than my counterpart in Austin, and I get a way less cost of living also. I also know that Austin has way more opportunities than Houston does, so I'm screwed if I ever want to leave this job. My personal situation matches the chart in the article.