God sat upon the Mercy Seat and filled the ark. The symbolism was not that the ark would represent God, but was the vessel upon and within that He would choose to place Himself.
Since, until the incarnation of Christ, no man had ever seen God, making the blood offering upon the mercy seat was representative of offering that sacrifice to God.
The belief that Mary is the Ark of the new Covenant is not one elevating her in any way to "Godhood" or "demi-Godhood", but is a statement that she is the (created, formed from the dust of the earth) vessel where God chose to place Himself. Though I can appreciate that somebody wouldn't want to attach that "title" to her, I, for the life of me, cannot fathom how one could deny the essential facts of the situation. Just as I can appreciate where one would be reticent to actually state the Nicene Creed, how a Christian can deny the facts that are contained therein escapes me.
I'm wondering, though, if the problem is not Marian but actually a Christological problem. (I'm speaking here generically about those who believe Christ is the Ark, not about you specifically)
If one believes that Christ was the Ark, then it follows that since the Ark was a created thing, then Christ was a created thing (or, at a minimum, His body was a created thing)...and then that God chose to dwell in and around that created thing. That flies in the face of orthodox Christian belief that Christ was eternally begotten of the Father (as opposed to being created by the Father) and that Christ chose to become incarnate (that is, become in the flesh), taking His flesh from Mary.
The extreme end of that belief is Arianism (that Christ was a created being and, though the son of God, was a mere man).
The slightly more moderate version is Nestorianism or some form of Adoptionism, which separates the divine and human nature of Christ into two separate "persons" or "natures" -- and that Mary only gave birth to the human "person" of Christ, the divine being assumed at some point after birth. (This flies in the face of the orthodox teaching of the hypostatic union: that the divine and human natures of Christ, though distinct, were unified in one substance and one person)
That's where I have a massive problem with the idea that the Ark was Christ.
So instead, there is no problem with God who can be placed in a little box?