The main difference is going to be wheels and is why Kia made the EX premium package to give you most everything the Touring has without the 18" wheels. The EPA ratings are based on weight categories in part. It is likely that the extra hundred pounds that premium package adds stays within the range of one of those categories. However, the extra hundred pounds will impact your mpg to a small degree. Just as will carrying a couple 50 pound sacks of salt in the back will. That extra weight will also impact your acceleration and braking.
A smooth roof is best (I actually removed the roof rails on mine) for best efficiency. So no doubt the bumps from the skylight will change your mpg but it would be unmeasurable outside of a wind tunnel. Personally, I'm against sunroofs. They reduce interior headroom, increase weight, added risks of leaks and wind noise and breakage, and cause a lot of injuries in rollovers (including ejection) and regulation is being weighed. Otherwise they are dandy, and for those who really enjoy them, I would think the small loss of efficiency would be not be top on your decision issues. So buy what you really like! The Niro will still get better mpg than anything else its shape. If you want absolute maximum mpg, you should be shopping Ioniqs and Prii. Or an EV.