You should not receive a duplicate Pirate Junkrat skin unless you already have all of the legendary Anniversary skins.
There is a notable caveat here, though – the contents of unopened loot boxes also count toward our check for duplicates. If a player buys the 50 Anniversary Loot Boxes + 1 Legendary Anniversary Loot Box pack, and they open the Legendary Anniversary Loot Box first, they might get a duplicate right away because the anniversary legendary skins they are missing are actually in their 50 unopened Anniversary Loot Boxes.
In the future, we’re going to change the order in which these boxes are generated, so that we generate Legendary boxes (which are more likely to be opened first) before non-Legendary boxes. This change should greatly reduce the frequency with which this confusion occurs.
Apologies for the confusion and hopefully this clears things up.