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If you do that, you'll have a permanent poop pile under the coop that you can't clean out...flies, odor, YUCK. Make sure the barriers are removable somehow.
I agree with using some type of 1" hardware cloth to cover the pit and smaller wire elsewhere, for safety's sake. 1" should be wide enough to allow the droppings to fall through. By all means, don't use chicken wire... Some predators can shred that stuff easily.
I think you should make a little wall (like, a foot or two high) in between the droppings pit and the rest of the coop. Otherwise, your bedding material on the coop floor will end up either falling through or blocking the pit opening.