You have it backwards! If you were to buy a sealed NES game, you have no idea if you have 5 or 3 screw version unless it has been determined how to tell just from the box. So in that case, it could be impossible to know if you had both a 5 and 3 screw version sealed.
The point I’m trying to make is that these two NES variants are mutually exclusive
always. It's not dependent on the condition of the game, if it's sealed or opened. Even though the box may be the same, there are fundamental differences between both versions and you can’t change from one to the other at will. You can't have both a 5 and a 3 screw in the same box, it's just not possible no matter what.
For Shantae, from a materialistic perspective it's the exact same game, with the same release time and artwork across the board, it only depends on which cover got used when the game was sealed. It’s only a mutually exclusive release if it’s sealed; once you open it, you have both, every single time. If theoretically everyone opened their copy of this game, this second entry would become completely pointless and obsolete. I think that's an valid indicator that this really isn't the best way to do it.
I think we can all agree that other games with reversible covers don’t get two entries in the database precisely
because they’re the same game. Therefore, I don’t think that because this one happens to be sealed when it’s put on the shelf, it makes a good enough argument for two entries, that’s all. But I do understand that this is a special example and should at least be discussed, I won't discredit that call.
And I personally think the notes section is a perfectly adequate method for a collector to indicate that they have more than one sealed copy with each artwork, I'm interested in hearing why that wouldn't be appropriate. Sealed collectors are already regulated to using the notes section by default on this site.
Going by your point above, one could also make an argument that we would then need a third entry in the database for every 3/5 cart NES game, with no variant attached to it at all, for people who have bought a sealed copy but have no idea what they have inside! I think that's a little silly, haha. I don't think this database has ever really catered to sealed collectors.