“And they don’t have her sitting on the mercy seat of the ark in the place of God either do they?”
No, they don’t. Notice there are no legs? She is not sitting on the mercy seat. She is above the moon OVER the seat. It is a visual analogy to Mary as the New Ark of the Covenant because she holds the Word made Flesh within her (shown as the Eucharist). Yeah, we all have eyes, but clearly some of us can see when a figure is shown ABOVE the mercy seat RATHER THAN SITTING ON IT.
Mary’s seat is not the Mercy Seat, but this one: http://en.wikipedia.org/wiki/Seat_of_Wisdom
Mary was beautifully prefigured by the Ark of the Covenant .
The Ark carried sacred objects --- flakes of manna and the tablets of the Law --- associated with God's saving work toward the Hebrew people. And Mary carried not manna, but the Living Bread; not the Law, but the Lawgiver; she carried not just the saving of the Hebrew people, but the Savior of the World.