For me it's more about locating the card. Large collections are broken up into binders and boxes. The inventory feature is cool, but I still need to worry about it's physical location. Great, so I know that I own a 9th edition Greater Good, but now I have to go find it.
The ideal solution for me is making it so that deck ideas pull cards from anywhere in your collection, so you know it *can* be built, but a built deck has specific cards in it. This way when I use the program, it could tell me which built deck the card is in. I could easily just call my boxes and binders large 'built decks' and get exactly what I want. When I click on Greater Good details it would tell me what built sets they are in. I'd know my foil copy of 9th edition Greater Good is in my Selvala EDH deck, and my regular one is in my EDH trade binder.
For database purposes it's probably best if you could label which sets were decks and which were not.