Only rares and mythics have duplicate protection, and the lowest rarity of the card on Arena is what counts for that. Also, only cards opened in packs will have that protection.

You got your first copy of that specific version, which you now have available as a full set due to your other copies. Additional copies will result in vault progress (if lowest rarity is uncommon or common) or gems (if lowest rarity is rare or mythic). But the first copy of a new version will not give vault progress nor gems, even if it is the 5th (or 100th) copy. That first copy is needed to acces that version in the first place.