Bought a Pathfinder from Rapid City last winter. Had to pay sales tax when I registered it. Other than that, I don't recall any special fees or extra expenses. For the money, I feel like I got a better deal there, but it was used, so hard to compare apples to oranges.
One thing to think about (I know you said you're looking at new), sometimes the dealers here in ND will offer to bring a used car from a dealership there, here, so you can look at it. I was looking for a late-model mid-sized SUV, and Dvorak in Bismarck offered to bring the vehicle from SD to here. It had just gone on the lot in SD though, so that dealer said no.
Gotta give the guy at Dvorak kudos for trying hard. I would have preferred to purchase in town, but it wasn't a deal-breaker.
My $.02.