$4.99 is cheap for that package- even the larger box is $4.99 to the customer as compared to a small flat rate USPS at $7+.
And, most of their costs associated with shipping and packaging come from reprints and refunds of parts that have been badly packed inside even those boxes. Just ask me how I know. I'd hate to see what wold happen to my prints if smaller packaging were used.
I have only seen two sizes of boxes (so far) regardless of the print size. This likely keeps their box and packaging inventory at a minimum, and keeps the decision on which size package to use out of the packers hands (believe me, this is a good thing).
Besides, those smaller boxes come in handy if you have to ship something. I re-use them and the bubble bags all the time.