That's always been a problem as ebay has not way of knowing what the new box size is going to be so combined shipping only changes the weight. In listings where that might be a problem, you could turn off combined shipping so that the buyer is charged the full shipping cost for each one. If it costs quite a bit less, you can give a partial refund to the buyer if you choose to.
I think that other sellers will figure out the shipping charge to the farthest destination that you ship to for one item and for multiple items. Then you could use a flat rate rather than calculated shipping. So for the first one you might charge $25 and for each one after that you might charge an extra $15.
