In a large bowl, combine the whole wheat flour, 1 cup all purpose flour, oats, brown sugar, baking soda, cinnamon, salt, all-spice, and nutmeg. Add the vegan margarine in small pieces, then quickly work it in with your fingers, until mixture resembles coarse crumbs. Press 2/3 of the crumbs into prepared baking dish. Evenly arrange the sliced apples over top.
Place rack in center of your oven and preheat oven to 350 degrees F. Line an 8-inch x 8-inch baking dish with parchment paper and spray lightly with nonstick cooking spray.