I agree. I think if you have to plan, doing it at Fontana right before you go in would be the best bet.
Keep in mind that not all delays are by the will of the hiker. For those of us who when through early, there's the worry of hitting snow in the Smokies. In the cases where it doesn't drive you off the trail, it could still but a damper on your mileage and ruin your schedule. I'd hate to have to push on from a half-empty shelter on a cold, snowy night just because I thought half a week ago that I'd be able to do the miles. Obviously, if the ranger is understanding its a problem, but one anal person could ruin the whole show.
I have no problem with paying the fees, just with the scheduling and reservations. Right now there is no money attached, so its far easier to let scheduling errors slide.
Just my 2 cents.