Beat butter, brown sugar, and granulated sugar in the bowl of a stand mixer fitted with a paddle attachment for 4-5 minutes until creamy and light.
Add eggs one at a time, mixing well after each addition, stopping to scrape the bottom and sides of the bowl. Stir in vanilla extract.
Add both types of flour, baking soda, baking powder, and salt. Pulse a few times to incorporate, then mix on low speed for 5 to 10 seconds, just until combined. Stir in chocolate.
Scoop the cookie dough into large 3 ½-ounce mounds on a baking sheet lined with parchment paper. They should be slightly larger than golf balls and placed close together. Sprinkle with flaky salt. Cover tightly with plastic wrap and refrigerate for at least 24 hours so the dough can chill and the flavors can develop. The cookies can be baked any time between the 24 and 72 hour mark.
When ready to bake, preheat oven to 350°F for at least 20 minutes. Line a baking sheet with parchment paper and arrange 6 balls of chilled cookie dough on it, spaced so there is room for the cookies to spread.
Bake for 18 to 20 minutes until golden brown but still soft in the centers. Remove from oven and cool for at least 10 minutes before transferring the cookies to a wire rack to cool. The cookies can be enjoyed right away while still warm, or you can let them cool completely and coat the bottoms with additional dark chocolate.
Line additional baking sheets with silicon baking mats. Melt the additional chocolate in the microwave on 50% power for 60-90 seconds, stirring every 30 seconds, until smooth. Spoon melted chocolate onto the bottoms of the cooled cookies and spread to evenly coat them in a thin layer. Place the cookies onto the baking mats with the chocolate coated bottoms down. Let them set up completely for the chocolate to harden before enjoying.