The Busse Combat site orders directly from Busse. You get to order any of the available options, for future production.
The Busse Company Store is an independent site run by a dealer (Skunk). He orders stuff that he thinks people will buy, and is stuck with it until they do. Fewer options, but immediate delivery, since he doesn't advertise an item until he has it from the shop. Skunk could have any number of arrangements with Jerry regarding cost, delivery terms, allowable markup, etc.
An analogy that comes to mind is Spyderco - you can order directly from Spyderco, or through one of their many dealers. Except that the spyderco factory store only advertises knives on hand (not future orders), and Busse only has one dealer (true, other dealers resell Busse knives, I'm not sure if they have special pricing arrangements or whatnot)
Busse Combat / Swamp Rat / Scrap Yard brands keep the different knife grades seperate. There may have been tax or business advantages to spinning these off as seperate companies, or Jerry may have just been distributing management labor. This isn't my area of expertise.