This needs to be added to the Wiki or make the option more obvious.
For those that may stumble on this post like me looking for it, I found another thread that mentioned it
here (with a pic in bonus). You need to be in List View, if you are in image view you will not see the option. (You can switch back to image view after that).
The way Allow reprint seem to works is that when you are selecting a set (For example a Duel Deck) if you select Allow Reprint at the same time it will look for all the other reprint for the same card instead of only the actual set you selected. With the show unique cards option enabled you will see only the newest variation.
Since the list of cards is processed when adding a filter, changing the show unique after the facts will only show the cards with the same name that were hidden.
As an example lets say you add a filter for a duel deck and do not select the allow reprint option it will show only cards from this set, toggling show unique cards will only show you the different lands variation included in the set, instead of only 1 for every name.
If you did check allow reprint, the pool of cards will include all the different variant for every card that this set includes. With the Show Unique Cards option on, you won't see a lot of difference at first because you still have only 1 card of each, sometimes from a different set. But when you disable the show unique cards option it will show every copy of every cards, like every version of every swamp that exists.
It seems that the Format filter does work as if you selected allow reprint, so if you want to play Standard with every variation that exists you can, but if you only want some set you will need to add a set filter also.
The problem seems to be that changing any options in the sets filter after the facts doesn't affect the filter at all. So you need to clear the filter before changing the sets list. In older versions of Forge adding a Set filter would actually do that (hence the name, add...) right now it seems to remember your choice but doesn't update the filter when you add new sets filters.