You are probably right that it wouldn't be a robust solution.I think you will regret this decision if you follow through on this.
Not only are you locking yourself out from all the rare cards that gets spoiled that doesn’t have an alt art. You are also doing the same to commons and uncommons alt art variants. I also believe that it doesn’t signal very well to the players. Don’t know if that is your intend.
Finally.. if you’re simply going to divide the cards are rarity then they already have a clear sign on the card: the set symbol color. I was thinking the solution to mark your cards was only relevant if you deviate from rarity splits.
I also agree that using native rarity would be ideal, but I was looking for ways to avoid constraining myself with it.