Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners and lightly spray the insides with nonstick cooking spray to help prevent sticking. Alternatively, you can skip the liners and generously coat the muffin tin with nonstick spray.
In a medium bowl, whisk together the flour, baking soda, cinnamon, nutmeg, and salt until well combined. Set this dry mixture aside. In a large separate bowl, combine the shredded carrots, maple syrup, applesauce, egg, oil, and vanilla extract. Whisk until the wet ingredients are well blended, then slowly add the milk and stir in the dry flour mixture until just combined—avoid overmixing.
If desired, gently fold in the shredded coconut and raisins. Divide the batter evenly among the prepared muffin cups, filling each one about 3/4 full. Bake for 18–20 minutes or until a toothpick inserted into the center of a muffin comes out clean. Let the muffins cool in the pan for about 10 minutes, then transfer them to a wire rack to cool completely.
Once the muffins have cooled, prepare the cream cheese glaze. Place the cream cheese in a medium microwave-safe bowl and heat on high for 10–20 seconds, just until it's slightly warm and soft. Stir gently, then add in the powdered sugar, vanilla extract, and 1 tablespoon of milk. Stir again, and if needed, add a little more milk until the glaze reaches a smooth, pourable consistency—not too thin, but not overly thick.
Dip the tops of each muffin into the glaze, then return them to the wire rack. If you like, sprinkle the glazed muffins with additional shredded coconut or chopped walnuts/pecans. This recipe yields 12 muffins.