I think how you categorize them would depend on if you're including additional info about the set or subset.
The ones where it's not really possible to tell if the card came from any particular product I don't see much benefit to listing other than the base set. But I would try to track what different products were issued.
For ones like the Donruss where the pack issued cards and the factory set issued cards are different I would track them as different sets.
Factory set exclusives I would also consider to be their own sets, just like so many other exclusives available only in a particular product, and often only from a particular retailer.
I think in some cases, it may be possible to tell factory set cards from pack issued cards, but it just isn't known because of lack of anyone keeping track or not even checking.
And, how crazy will you get tracking production diffrences.
Like the 3 different die cuts on 88 Score, Three different ways gloss was put on the backs of 93 Upper deck, other years besides 91 Topps having backs that react to UV... etc.
I don't think it matters much which method you use, as long as it stays consistent so you don't have things like "i list only these sorts of things, in this way except 91 topps which is a complete mess so I list it a different way"
I've been considering doing a catalog that covers that stuff, and the method I like is used by one of the stamp catalogs. For complex issues they show the basic set, with usually the very obvious differences. The next two or more pages are the "detailed listing" which includes differences that are far less obvious, and rarely, further info about where to find even more detailed information for specialists - One set has a book showing hundreds of plate flaws. So may they had to come up with a location coding scheme... Yeah, even I think thats crazy, but I own that book, so....
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