GDP is barely mentioned, as one of many metrics they look at. And he acknowledges many issues entailed in urban living. You seem to be pushing against a point the article isn't making.
Whenever he talked about 'wages' or anything like that, it's de-facto talking about GDP. All economic value in an economic zone = GDP. (roughly).
i.e. 'Cities have higher wages' etc. Well, the statement is false depending on how you value wages via their purchasing power of things like 'silence' and 'clean air'.