Let me just make sure I understand your need correctly.
Say you do want 1x Cryptic Command from the Invocations for your Egyptian-themed EDH deck, but you also have two other EDH decks that require Cryptic Command. For those, you merely want the artwork that is used for Lorwyn / Modern Masters / Modern Masters 2015, but you don't care about edition.
You would want to be able to input them into your wishlist as follows:
1 | Cryptic Command | Invocation
2 | Cryptic Command | LRW or MMA or MM2
You would NOT want to input it as follows...
1 | Cryptic Command | Invocation
1 | Cryptic Command | LRW
1 | Cryptic Command | MMA
1 | Cryptic Command | MM2
...because you only need 2 copies of the non-Invocation artwork, not 3 copies.
Is that the idea?
I believe that anytime you offer a user more granular control, it's better. So I'm all in favor of this change. That said, I bet it would entail fairly foundational changes to Deckbox's database tables and SQL queries, so it would probably be a long time coming. But still a great idea!