Preheat oven to 350 degrees F. Line a 12-cavity muffin pan with cupcake liners and set aside. In a medium-sized bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, and nutmeg. Set aside.Pour batter into the prepared muffin cups, filling each cup about 3/4 full. You should use all of the batters between 16 cavities. Bake in preheated oven about 18 - 22 minutes or until a toothpick when inserted into the center of cupcake comes out clean. Cool in muffin tin several minutes then transfer to a wire rack and cool completely. In a separate large mixing bowl, using hand mixers, beat together the butter, brown sugar, and white sugar until smooth and creamy. Mash over-ripe bananas and measure to make sure you have exactly 3/4 cup. Beat in the bananas to the batter until smooth. Add in the full egg, egg yolk (reserve whites for another recipe/omelets throughout the week or discard), and pure vanilla extract. Beat until smooth.
Add the dry to the wet ingredients alternating additions with the buttermilk (Add half the dry, half the buttermilk, rest of the day, rest of the buttermilk). Beat after each addition JUST until the ingredients are incorporated being careful to not overmix.
Pour batter into the prepared muffin cups, filling each cup about 3/4 full. You should use all of the batters between 16 cavities. Bake in preheated oven about 18 - 22 minutes or until a toothpick when inserted into the center of cupcake comes out clean. Cool in muffin tin several minutes then transfer to a wire rack and cool completely.