Preheat oven to 350° F. Place cupcake liners into muffin tins, or spray each cup with a bit of cooking spray.
Combine oats and milk in a small bowl, set aside for 5-10 minutes.
In a large bowl, combine flours, baking soda, baking powder, cinnamon, nutmeg, and salt.
In a medium bowl, combine pumpkin, applesauce, eggs, and maple syrup.
Add pumpkin mixture and oat mixture to the large bowl with the dry ingredients; stir until fully combined.
Divide batter among muffin cups, filling each 2/3 full.
In a small bowl, combine pumpkin seeds and 1 tablespoon maple syrup. Put small spoonfuls or pinches of this mixture on top of each muffin.
Bake for 20 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Allow to cool before serving.