It's interesting that some of the highest and lowest after-rent salaries are in the Bay area. That's a pretty clear indicator of SF's constrained housing supply in particular. It's also interesting so many low ranked after-rent cities are in Florida, which might reflect a strong desire to live there despite the lack of job opportunity.
I'd bet the difference in those two statistics indicates uneven housing supply (residential areas aren't the same as business areas) and small cities (residential areas are counted differently than business areas).