Well, I explained exactly why it happens. It's just duer to how its programmed. They needed a skill boost on the amulet, and must have thought "hey, let's make it give +3 to Wisdom," resulting in them making the "skill bonus" slot on the item another Wisdom.
A lot of unique jewelry that formerly had a skill bonus now have two, such as Jagon's Necklace (the Mindread +1 is due to the same effect), as is the Fireball bonus on Lovis' Amulet.
So my answer was basically that no, they intended the amulet to have +3 Wisdom total, but added the extra point of wisdom in due to what I assume are the constraints of the item system and how the game keeps track of items.
