Move the oven rack to the middle position. Preheat oven to 425°F (220°C). Grease one standard 12-count muffin pan with nonstick spray or line it with muffin papers. Set aside.
In a large bowl, whisk together the 3 cups all-purpose flour, 1 tablespoon baking powder, 2 teaspoons cinnamon, 1 teaspoon baking soda, ½ teaspoon nutmeg, and ½ teaspoon kosher salt. Toss the 2 cup peeled and diced apples in the dry ingredients until they are well coated. This will prevent the fruit from sinking to the bottom of the muffins. Set aside.
In a medium bowl whisk together the ½ cup granulated white sugar, ½ cup brown sugar, ⅔ cup vegetable oil, 2 large eggs, 1 egg yolk, and 1 teaspoon vanilla extract. Stir in the 1 cup sourdough discard.
Pour the wet ingredients into the dry ingredients and fold them together gently with a spatula until just combined. Do not over mix. The batter will be thick. Allow the batter to rest for 5 minutes.
Divide the batter between each muffin cup, filling all the way to the top.
Bake the muffins at 425°F (220°C) for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (180°C) and continue to bake for 20 minutes until the tops are golden brown. Use a toothpick to test for doneness. Insert a toothpick into the center of a muffin, if it comes out clean, the muffins are done.
While the muffins are baking prepare the topping. Melt the ¼ cup butter in a microwave-safe bowl. In a separate bowl mix together the ¼ cup granulated white sugar and 2 tablespoons ground cinnamon.
Allow the muffins to cool for several minutes in the muffin pan. Remove a muffin from the pan, brush the top with the melted butter and then sprinkle with the cinnamon-sugar mixture. Place the muffins on a wire rack to cool completely.