Preheat oven to 350°Line an 8x8 inch baking dish with parchment paper and set aside. For thicker bars, use a 9x5 loaf pan instead. Set baking dish aside.
In a large bowl, whisk together the coconut flour and almond flour then add the melted coconut oil and maple syrup and stir with a rubber spatula until no clumps of flour remain.
Add the shortbread mixture into the pan and pack it down tightly with a rubber spatula to all corners of the pan. Coat the spatula with a little melted coconut oil if the shortbread mixture is sticking to it too much.
Bake shortbread for 10-12 minutes, or until it starts to turn golden brown. Allow to cool completely. Place in the fridge or freezer to speed up the cooling process.
While the shortbread is cooling, make the caramel layer. In a medium-large bowl, combine the almond/cashew butter, coconut oil, maple syrup, vanilla and salt. Mix with a rubber spatula or whisk until smooth. If needed, microwave on high for 10-15 seconds to make mixing easier. Pour the caramel over the cooled shortbread and place back in the fridge or freezer to set and harden. Refrigerate for at least 1 hour or 30 minutes in the freezer.
Once the caramel layer is almost set, start on the chocolate layer. Whisk together all of the chocolate ingredients until smooth and pour over the cooled caramel layer. Smooth evenly then top with flaky sea salt. Let cool in the fridge or freezer again until set. Slice into 1-inch slices. Keep store in the refrigerator or freezer.