At the moment, we have no way to select different package types based on the quantity ordered. You can either configure your products with the smaller box type (and consolidate multiple smaller boxes ordered into a larger box for actual shipping), or configure with the larger box type (and downgrade to a smaller box when warranted); either way, you'd probably come out a bit ahead on shipping costs vs. charges, so you could simply pocket or refund any difference.
This next suggestion may not be exactly what you had in mind, but I think it's as close as we can get at the moment to what you described. For our "Tube" container types, our system knows to consolidate products that ship in any Tube container into the largest such container specified for any product in the order, up to the packaging capacity specified -- our original idea here was that an order containing some posters that ship in a small tube and some that ship in a large tube should just ship them all together in one large tube, but you can take advantage of this technicality even if you're not literally using tubes or selling posters. :^)
E.g., if you have Product A set to ship up to 4 units in a Small Tube, and Product B set to ship up to 4 units in a Large Tube, then an order placed for 2 units each of Products A and B would only add the cost+weight of one Large Tube (as B's container had 2 "slots" left unoccupied, so those could be occupied by 2 units of A).