Hey Jonnie,
I did something similar to what you are asking for your '12 SERG on my '12 SESG. I didn't care for the stock seat on my '12 and went with a sundowner seat. Yes, it fit over the rails and did not damage them. I put about 24,000 miles on the Sundowner with no visual issues on the rails. It does rub in front of the rails a bit but I always keep a good wax on that area and make sure to remove the seat and clean that part of the fender each wash so no big issues. When I traded it this past Summer, I removed the Sundowner and put the stock seat back. The new owner was none the wiser since it all looked great when they removed the passenger pillion....rails and paint looked fine.
I believe there were some issues with other than stock/non-hd seats and the fender rails but I can't speak to that, only the experience I had with the Sundowner.
Good luck