Position racks in the upper and lower thirds of the oven and preheat to 350 degrees F (180 degrees C). Line 2 rimless cookie sheets with parchment paper.
Place the Unsalted Butter (6 tablespoon) in a small, heavy-bottomed saucepan set over the lowest possible heat. Add half of the Bittersweet Chocolate (6 ounce) and melt together, stirring frequently to prevent the chocolate from scorching
Continue cooking until the mixture is pleasantly warm, but not super hot, to the touch. Remove from the heat and keep warm. Whisk together the Tapioca Flour (2 tablespoon), Buckwheat Flour (1/2 cup), and Baking Powder (3/4 teaspoon) in a small bowl and set aside.
Meanwhile, place the Egg (2), Organic Cane Sugar (1/2 cup), and Fine Sea Salt (1/2 teaspoon) in the bowl of a stand mixer fitted with the whisk attachment and whip on medium-high speed until the mixture triples in volume and is very light and fluffy, 5 minutes.
Turn the mixer to low and stir in the Vanilla Extract (1 teaspoon) until just combined, then the warm (but not too hot) chocolate/butter mixture. Add the flour mixture and beat on low speed until combined. Remove the bowl from the mixer and use a flexible silicone spatula to fold in the remaining chopped Bittersweet Chocolate (6 ounce).
If the batter is very runny, let it cool for a few minutes until it firms to the consistency of a thick brownie batter. Use a #40 spring-loaded ice cream scoop or 2 spoons to drop heaping tablespoons of batter onto the prepared baking sheets, spacing them at least 2-inches apart. Top each cookie with a few chunks of chocolate and a few flecks of Sea Salt Flakes (to taste).
Bake the cookies until puffed and cracked and the edges are set, 8–12 minutes, rotating the pans front to back and top to bottom halfway through baking.
Let them cool completely on the pans. Serve and enjoy warm or room temperature.