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Preheat oven to 375ºF.
Spray a 12-count muffin pan with non-stick spray (see notes if using liners).
In a small bowl, soak the raisins with the ¼ cup hot milk while you prepare the other ingredients.
In a large bowl, whisk together spelt flour, oat flour, cinnamon, nutmeg (if using), baking soda, and salt.
In a separate bowl, combine the eggs, coconut oil, applesauce, brown sugar, and vanilla. Whisk until smooth and emulsified. Stir in the grated carrots, apple, shredded coconut, walnuts, and raisins with the milk.
Use a spatula to fold the dry ingredients into the wet ingredients until the batter is weel combined, but do not overmix.
Divide the batter evenly among the wells of the prepared muffin pan, filling all the way to the top. Sprinkle the tops with pepitas, if using.
Bake for 23 to 25 minutes or until a toothpick inserted in the center of a muffin comes out clean. (See notes for achieveing a bakery-style domed muffin).
Allow the muffins to cool in the pan for 10 minutes then transfer to a wire rack to finish cooling before serving.
Leftover muffins can be stored at room temperature for up to 2 days or in the refrigerator for 1 week.