JAE,
Well, we all know (or should know) the metal deck is used to be part of the tension steel in composite deck. Therefore, if the manual is calling out WWF in addition to the composite metal deck, or to reduce the loads by 10%, by deduction the form deck w/o reinforcing is a screwed up situation. I'd probably make them remove the concrete and put it down the way I spec'd.
You could potentially calculate the cracked moment of inertia for a 12" wide concrete section for your design loading condition. Given your deflection at midspan has to be exactly the same between the metal deck and the concrete, you could determine how much of your design load is carried on your concrete and how much is carried on the metal deck. It would be similar as designing a flitch plate beam. (I think) There just isn't anything between the concrete and mtl deck that would cause the mtl deck to go into tension, so you would have to design it in bending. This is making my head hurt.