1. MAKE THE FILLING: In a medium mixing bowl with an electric hand mixer, beat 8 ounces softened cream cheese, 1 cup confectioner's sugar and 1 teaspoon vanilla extract until smooth. Set aside.
2. MAKE THE MUFFIN BATTER: Preheat the oven to 350 degrees. Line 12 JUMBO muffin cups with foil or paper liners.
3. In a large mixing bowl, whisk together the flours, flaxmeal, baking soda, cinnamon, allspice, cloves and salt.
4. In another large mixing bowl, whisk together the sugar, oil, eggs and vanilla. Fold in the grated carrots, crushed pineapple and applesauce.
5. Add the flour mixture to the carrot mixture; stir just until moistened.
6. Fill each muffin cup almost to the top. Place a 1 tablespoon of the reserved filling in the middle of each muffin. Use a cookie scoop for ease. Bake for 25-35 minutes or until a tester comes out clean. Cool in the pan 10 minutes and then remove to a rack to cool completely before storage in the refrigerator. Sprinkle with turbinado sugar to serve.