Preheat oven to 400 degrees. Grease the wells of the doughnut pan with some butter.
In a glass measuring cup, mix together milk and vinegar and allow to sit at room temperature for at least 5 minutes to curdle.
In a large bowl whisk together flours, cocoa powder, baking powder, nutmeg and salt.
In a small bowl, whisk together melted butter, sugar, honey, egg, vanilla and curdled milk.
Whisk wet ingredients into dry ingredients, taking care not to overmix.
Spoon batter evenly into wells of the doughnut pan, filling only 2/3 full.* If filled too high, there won’t be any doughnut holes. Another way to fill the wells is by transferring the batter to a quart-size Ziploc bag and snipping one corner ½inch and piping the batter into the wells. Bake for 8-10 minutes or until doughnuts spring back when pressed lightly. Allow to cool 5 minutes before turning doughnuts onto a cooling rack. Donuts can be glazed when they are slightly warm or cool.
Make the glaze: In a heat proof bowl, combine glaze ingredients and set over a small pot of simmering water. Stir regularly until ingredients are melted and smooth.
Dip tops of donuts in glaze and place glaze side up on a wire rack to allow glaze to drip. Sprinkle immediately with toppings, if desired.