Reading the article makes it clear what's going on here, although you have to get to the end. I had the same reaction to the idea of Tahoe and SF being consider

Reading the article makes it clear what's going on here, although you have to get to the end. I had the same reaction to the idea of Tahoe and SF being considered part of the same "megaregion", since while someone may drive from Tahoe to SF on an irregular basis, the number of people doing it everyday must be miniscule. So I read deeper to try and understand the basis of these things. TL;DR -- they arbitrarily chose 50 as the number of regions to consider. Everything above a certain threshold gets associated with some sort of region, and then they did basic clustering to see which commutes get assigned to which region. So in my Tahoe example, more people are commuting from the Tahoe area to Sacramento than to Reno, so Tahoe ends up associated with the entire SF Bay Area megaregion instead of with Reno, which it's geographically much closer to. If there had been more regions, Sacramento would have gotten its own region most likely.