Preheat the oven to 350ºF. Grease a 12-cup muffin pan and set aside. Combine the flax and water and set aside to gel, forming a “flax egg.”
Whisk together the flours, quinoa flakes, sugar, baking powder, and spices in a large mixing bowl.
In a separate bowl, beat together applesauce, pumpkin, milk, molasses, syrup, and vanilla. Whisk in the flax egg. Pour the wet ingredients into the dry. Stir to thoroughly combine (the batter will be kind of thick, but still stirrable and soft).
Fill each cup ¾ full. Add water to the unused cups. Sprinkle the tops of the muffins with turbinado sugar, if desired.
Bake on the center rack for 23-26 minutes, until a cake tester inserted into the center comes out clean.
Cool in the pan for 5 minutes, then transfer to a wire rack and cool completely. If desired, reheat in the toaster oven or in the microwave.