It affects tech cost scaling (cheaper) and city maintenance expense (higher), as well as things like how many cities Representation gives happiness to and how many Universities you need to build Oxford, for example. The difference in tech costs is most relevant right at the start, since I had my sandbox set to Standard size and chose starting techs accordingly.
EDIT: I hopped in again and the other settings all look good.
EDIT: I hopped in again and the other settings all look good.