i wouldn't be surprised if Wayne tower ends being another building in the next one - or Akrham being in a different part of town in Gotham.
To be fair, it's the same Gotham, minus the Narrows really (and the Wayne Tower changes). CGI was still used to make the Chicago looking very vast in some shots, and to make Lake Michigan into the Atlantic. Check out the links for more details (It's not just Chicago with any enhancements)
I think the point being is that Nolan wanted Gotham to be a nice looking town, but very cold. The grit comes from the characters.