But Baltimore is our example of how to take a city you know (or sorta-know) and Dresdenify it. So our "sample campaign" is Baltimorean, but our "NPCs from the books" writeups are Chicagoan, etc.
Yes, and this makes sense from a RPG development standpoint because...
1. We don't want the RPG to conflict horribly with anything that Jim may write in the future. We have to just hope that he doesn't read the RPG and then decide to have Harry relocate to Baltimore 'cuz it's so cool!
2. The assumption is that players will make up their own Harry-like characters, and probably will not be playing Harry, so it doesn't need to be set there anyway.
3. If the campaign takes place down the street from Harry (or anywhere near Chicago) there will always be the feeling that Harry might appear and save the day as needed. This stinks of railroading and sucks the life out of the drama of the story.
So ... by developing Baltimore we produce a RPG that has a built-in setting, plus one can use the novels as a sourcebook for another setting. Kind of like "buy one, get one free...."