Preheat oven to 350°F (177°C). Line a 12‑cup muffin pan or grease it well.
In a bowl, mix flour, baking soda, cinnamon, nutmeg, and salt.
In another bowl, whisk carrots, maple syrup, applesauce, egg, oil, vanilla, and milk.
Combine wet and dry ingredients. Mix until just combined. Fold in optional mix‑ins.
Divide batter into muffin cups and bake for 18–20 minutes, until a toothpick comes out clean.
Let cool for 10 minutes, then transfer to a rack.
For glaze: warm cream cheese slightly, mix with powdered sugar, vanilla, and milk until smooth. Dip muffin tops into glaze and let set before serving.