If anything, I think SE should make it so Rare drops you get in your box that you ALREADY OWN can be bumped into the Treasure Pool.

That coupled with faster fights and higher drop rates would probably come pretty close to fixing the issue entirely, while still maintaining the integrity of the system as intended.

Make it so when you select to obtain the item from the box, the game detects the RARE conflict and automatically resolves the conflict using the treasure pool. Shouldn't be THAT hard to special-case it for Voidwatch boxes.