Preheat oven to 350°.
Combine first 3 ingredients in a large bowl. Sprinkle apple mixture with granulated sugar, cinnamon, and nutmeg; toss well. Combine milk, molasses, and vanilla in a medium bowl. Add bread to milk mixture; toss to combine. Add bread mixture to apple mixture; toss to combine. Spoon bread mixture into an 8-inch square baking dish coated with cooking spray.
Lightly spoon flour into a dry measuring cup; level with a knife. Combine flour and brown sugar; cut in chilled butter using a pastry blender or 2 knives until mixture resembles small pebbles. Sprinkle brown sugar mixture over apple mixture. Bake at 350° for 40 minutes or until golden and bubbly. Serve warm.