It tends to crack the epoxy on the inside. In the long run it's another rust point. In reality that particular spot tends not to rust through as it dries pretty easily.
This is the reason you should use a wood block and not a rag. Think about it, you are lifting more than 1/2 the weight of the car (i.e. over 1500 pounds) with a piece of sheet metal. Spread it around a bit!