Dan, the Heroes/Men of History series is a good example (or for the baseball minded, the T206 series). Each of these series have all the cards of the series issued with different advertisements on the back. For the Heroes/Men of History there are 5 different advertisements on the back.
So the Heroes set could look like this:
CARDS
Included Sets (or maybe "Back Variations" or "Brand Variations")
Royal Bengals Little Cigars
Mners Extra Smoking Tobacco
Pan Handle Scrap
National Leaf Scrap
Blank Back
This doesn't address the issue of "Basic Set" vs "Master Set". Some (like me) don't care what advertisement is on the card. If I have a card, regardless of the advertisement, I consider that spot on the checklist filled (Basic Set). Some collectors only want National Leaf Scrap backs (they are the coolest looking and the rarest) and some collectors want one of every back variation (master set). So the example you listed isn't the perfect solution, but I thought it a step in the right direction. A couple weeks ago, Admin sent me a message saying that currently the database is not set up to handle "basic" vs "master" sets. I've started putting the variation descriptions in the release notes for some of the less confusing series.
That is an abbreviated version of a very undeveloped idea. A lot of the tobacco sets get really confusing, especially after the formation of the American Tobacco Company in 1891. Its almost like they didn't even think about the people that would be collecting these cards 125 years after they were issued.
My two-cents is worth slightly more than a penny.
-- Chad --