Heat oven to 375°F; butter a 9-by-13-inch baking dish.
Toss apples with brown sugar, 2 tablespoons flour, lemon juice, cinnamon, nutmeg, and 1/4 teaspoon salt. Spread evenly in dish.
Whisk remaining flour, granulated sugar, baking powder, and 1/2 teaspoon salt; cut in butter.
Stir in milk; turn soft dough onto floured surface. Pat 3/4 inch thick.
Cut rough 3-inch squares; arrange over apples with small gaps.
Bake 48 to 50 minutes until apples are tender, juices bubble, and topping browns. Rest 20 minutes.