The reason people put the spacers between the skid plates and frame is because they have lifted their Jeep and now it has vibrations in the driveline. By lowering the skid plate it corrects the angles and the vibrations go away. Some use a stack of washers from your local auto parts store, others use poly or metal spacers.
It's true that rust often forms there between the skid plate and the frame. The best solution for that is to remove the skid plate, sand down the skid plate areas with rust and the frame, prime with self-etching primer and paint with Krylon semi-flat black.