In a large bowl, mix together the flours, maple sugar, baking soda and powder, and salt.
In a medium bowl, whisk together the eggs, ghee, coconut milk and vanilla extract. Pour the wet ingredients into the dry ingredients and mix until well combined. Batter should be slightly thick.
Use an ice cream scoop to scoop the batter into 10 or 11 lined muffin cups. Bake for 25 minutes or until a toothpick inserted in the middle of a cupcake comes out clean. Place cupcakes on a cooling rack to cool completely before frosting.
Place the softened butter in a stand mixer fitted with the flat beater attachment. Whip on high speed until fluffy, scraping down the sides every minute or so, about 5 to 7 minutes—the longer, the better.
Add the vanilla extract and coconut milk and beat for another 2 to 3 minutes, until fully combined.
Turn the mixer off, add 2 tablespoons of the powdered sugar, and then turn on the mixer and process to combine. Repeat until all the powdered sugar has been added and the frosting is thoroughly whipped. Set aside.
For the apples
Place a large saute pan over medium heat. Add ghee along with the diced apples. Let cook and soften for about 10 minutes, tossing every couple minutes. Then add apple pie spice and cook for about 2-3 minutes. Once apples are soft and tender, add 3 heaping tablespoons of the caramel sauce and mix to combine. Set aside.
To build the cupcakes
When cupcakes are completely cooled, use a spoon to add frosting to each cupcake. (I like to build my frosting a little higher on the outsides so the toppings can sit in the middle without moving) Add about 1 teaspoon of caramel sauce to the middle of the cupcake then add about 1 tablespoon of the apple mixture on top. Continue until all cupcakes are frosted and topped! Serve immediately!