Preheat your oven to 375°F (190°C) and place the rack in the center position. Line a standard 12-cup muffin pan with paper liners or lightly grease each cup with non-stick spray.
Peel, core, and dice 2 medium apples into 1/2-inch cubes (about 1 1/2 cups). Pat the apple pieces dry with a paper towel to remove excess moisture and set aside.
In a small bowl, combine the streusel flour, sugar, and cinnamon, then rub in the cold butter pieces with your fingertips until the mixture resembles coarse, clumpy sand. Refrigerate until needed.
In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg until evenly combined. Make a well in the center and set aside.
In a medium bowl, whisk the eggs and sugar together until slightly pale, then add the oil, milk, sour cream, and vanilla extract and whisk until smooth and fully combined.
Pour the wet mixture into the well of the dry ingredients and fold together with a rubber spatula just until no dry flour streaks remain — do not overmix, as a few lumps are perfectly fine.
Gently fold the diced apple pieces into the batter using as few strokes as possible until evenly distributed throughout.
Divide the batter evenly among the 12 prepared muffin cups, filling each about 3/4 full. Top each with the chilled streusel topping (or the cinnamon-sugar mixture), pressing it gently to adhere.
Bake at 375°F (190°C) for 18 to 22 minutes, until a toothpick inserted into the center of the largest muffin comes out clean and the tops are golden brown. For tall domed tops, bake at 425°F for the first 5 minutes, then reduce to 375°F for the remainder.
Let the muffins cool in the pan for 5 minutes, then transfer to a wire cooling rack for at least 10 more minutes before serving warm or at room temperature.