I just want to add that some people add the extra shipping cost into their item price for the larger sizes. But as Pat said, otherwise, you either have to come up with an average or use the highest and refund for the smaller sizes. That means putting in the larger dimensions and weight for calculated shipping.
Admin has said they plan on working on variations in the new year - there are a number of things with them that need work and one is this shipping problem.
The problem is the same for the other shipping method as well - only one shipping cost or profile can be attached to any one listing.