It makes sense when you consider a couple of things.
They really want to go up Brasstown Bald in the NE part of the state. Well, due to the length of the race, this precludes them from venturing too far south. The organization caught a lot of grief for including too many lengthy car transfers between stages (which is unfair when you consider that they literally threw the route together with less then 80 days to spare in 04). To prevent those long car transfers (driving long distance from one finishing town to the next starting town), they have to keep it as compact as possible.
They hod no choice but to go back to Alpharetta after that City received an award for having the best Special Event in Georgia.
Because of the revenue the race brings to host cities, there are a lot of cities begging for the right to host the race, but terrain and distance dictates a lot of it.