Though I met plenty of people at ND who told me they were from Chicago, rather than DeKalb, Rockford, etc., so I guess why not.

the entire MSA was included, at least from what I could tell.

ETA: I think this helps Chicago in this type of calculation - it seems like every suburb has its own brew-house/restaurant in its little downtown, and Chicago has a lot of suburbs.

Chicago's beer scene is odd to me. It's spread out, as you mention, which makes it hard to feel much of a beer community whenever I'm in town. Cities like Portland and Denver tend to have concentrations and pockets of breweries and beer bars that make it easy to get a feel for their beer scenes. Maybe those exist in Chicago and I've just had poor tour guides.

and a few others that come to mind (probably Austin, Grand Rapids area) still out-punch the big cities pound for pound by a good bit.

The well-known breweries actually in the city (Half Acre, Revolution, DryHop, Haymarket, maybe a few others) tend to be clustered where gentrification started occurring maybe 10 or 20 years ago, and land was relatively still cheap in those areas, at least compared to today and compared to what were the expensive areas back then. You can almost draw a semi-circle arc around where that was at the time and go right through the first line of brewery renaissance in the city. That line has now pushed out again into areas like Humboldt Park, Edgewater, Hermosa, almost into Belmont Cragin - would have been unthinkable ten years ago, but that's where the cheap land is now, and it's too expensive to do anything where the more established places are. I think that's why you don't see a cluster or a couple of clusters.