Preheat oven to 400 degrees F (200 degrees C). Spray 12 muffin cups with cooking spray.
In a bowl, mix together the 2 flours, flax seed meal, rolled oats, baking powder, baking soda, salt, cinnamon, ginger, cloves, and nutmeg until the ingredients are thoroughly combined.
In another large bowl, beat together the brown sugar, pumpkin puree, yogurt , eggs, molasses, applesauce, canola oil, vanilla, and until well-blended. Stir in the flour mixture just to combine, and gently mix in the raisins and walnuts.
Divide the mixture into the prepared muffin tins, sprinkle each muffin with a few rolled oats and pumpkin seeds, and bake in the preheated oven until the tops spring back when touched and a toothpick inserted into the center comes out clean, 15 to 20 minutes.