No! The buyer pays whatever the listing says what they should pay.
If it turns out that you can ship for less you can either stick the extra money in your pocket as a "handling fee" or refund the excess to the buyer (note that YOU will not get a refund of FVF's from eBay).
Generally speaking the only time you would contemplate a partial shipping refund is when you have a combined order.
It looks like you use Calculated shipping, the buyer purchased knowing what the shipping is I don't see any reason to provide any type of refund just because you found slightly smaller or lighter box.
One day you'll have a shipment that will need a larger and/or heavier box than you thought, you'll be ok since you know you made a little extra on another shipment.
