They did though. The Bay Area is a lot more Balkanized than most urban areas for topographic reasons but for example they include St. Paul and Minneapolis one city despite being separated legally. I’m sure the other major cities have lots of little satellite cities included in the analysis too, they’re just not famous enough to be called out that way.

And yes there are some differences but there are a lot of similarities. Especially culture, weather, etc. When looking at the different places across the country, Bay Area cities are relatively similar with a few outlier exceptions.