In a saucepan over medium heat, melt the butter, swirling the pan occasionally.
Once melted, continue to heat and swirl the pan (it will start to bubble and crackle at this stage). Scrape the sides and bottom of the pan with a silicone spatula to unstick any brown milk solids that have formed. Continue cooking until the butter reaches a deep amber color and emits a nutty aroma.
Immediately transfer to a large heatproof bowl being sure to include all the brown bits/milk solids. Allow it to cool for 15-20 minutes while you chop the chocolate and prepare the other ingredients.
In a medium bowl, whisk together the spelt flour, tipo 1 flour (or whole wheat pastry flour), baking soda, and salt. Set aside.
Once the butter has cooled, whisk in the brown sugar and granulated sugar.
Add the egg, egg yolk, and vanilla extract. Whisk to combine.
Using a silicone spatula, fold in the flour mixture until just combined. It might seem like a lot of flour at first, but it should come together after a minute or so.
Fold in the dark chocolate until combined.
Cover the bowl with plastic wrap and chill in the fridge for 30 minutes or overnight.
Meanwhile, preheat the oven to 350°F (180°C) and line a large baking sheet with parchment paper.
Using a 3 tbsp cookie scoop, measure the cookies and place them onto the prepared baking sheet 1 ½-2 inches (4-5 cm) apart.
Bake for 12-14 minutes or until the edges are golden brown and the centers look slightly underdone.
Cool on the pan for 5 minutes before transferring to a wire rack to cool completely.
Sprinkle with flaky sea salt if desired.