I had the opportunity to visit two Hobby Lobby's yesterday and experienced the following:
If the store does not have the small box in stock (on the shelf), they cannot order another one. They are required to order the entire "nested" three box set. They will not order an entire set if there is one or two of the other sized boxes on the shelf.
The "nested" set is available online, but not the one small box.
The small box dimensions are 7-3/4" x 3-1/4" x 5-1/2".
An alternative box can be had at a cigar store. One nearby to me has a large collection available for sale, of various shapes and sizes. I found a "Black Market" cigar box with some personality, and similar dimensions.
With some modifications I hope it'll be adaptable to the new kit.