Full transparency: The costs all come down the cost of manufacturing. Since the all-in backers on this campaign only receive one box, the manufacturing cost is less. The cost of manufacturing the upgrade kit is actually higher than the base game, and we decided to reduce the upgrade kit's price below the base game to give previous backers a discount.
A box is typically the most expensive component in the games, and you'll have the fancy boxes that new explorers do not have. :) If you'd prefer to wait for the small box Revenge for a lower price, it will be available in retail soon after this campaign fulfills.