The wood case looks totally factory original to me. There are several pictures of the factory cased sets in the Standard Catalog of Smith & Wesson. The case in the original post has hinges, latch, case corners, accessories, support for the cleaning brush... that look like the original cases in the book. I have always wanted to own an original combo set.
There doesn't seem to be many rules on these combo sets. My guess is there were several factory runs of these sets and they may have followed different rules for each run. The sets could also be custom ordered in any combination the owner wanted. There is a picture of a double action gun that is in the same factory case with extra barrels and accessories in the above mentioned book. It says it is a factory set. On those custom orders they were probably taking a gun that was already made and in stock, and adding the extra barrels, sights, accessories... to complete the set.
Its interesting the revolver does not have target sights. If the buyer could afford a combo case with extra barrels, they could probably afford target sights on the revolver too, but who knows for sure.