Prepare the baking sheet. Preheat an oven to 350°F (177°C), then line a baking sheet with parchment paper.
Make browned butter. Add 14 Tbsp (180g) cubed unsalted butter to a medium saucepan over medium heat. Allow the butter to melt, then continue cooking for an additional 5-10 minutes, stirring constantly. You should see the butter begin to foam vigorously – keep stirring. Once the butter begins to turn golden brown and smells nutty, it’s done. Transfer the browned butter to a large mixing bowl before the milk solids burn (and be sure to use a spatula to scrape out all the browned bits!). Whisk in 1 heaping Tbsp white miso paste until well mixed. Allow the butter mixture to cool slightly, at least 5 minutes.
While the butter cools, mix the dry ingredients. In a medium bowl, whisk together 1½ cup (200g) all-purpose flour, 1 tsp baking powder, ¾ tsp baking soda, and ¼ tsp Kosher salt.
Mix the wet ingredients. To the cooled brown butter miso mixture, add ¾ cup (150g) brown sugar and ¼ cup (50g) granulated sugar, then whisk well to combine. Add 1 large egg and 1 Tbsp vanilla bean paste, then whisk vigorously for about 1 minute. The mixture will lighten in color and become very smooth.
Fold in the dry ingredients. Add the dry ingredients all at once, then use a spatula to gently fold into the wet ingredients until only a few streaks of flour remain.
Add chocolate. Pour in 6oz chopped dark chocolate, then fold to fully combine.
Portion the cookies. Use a cookie scoop (1-ounce) to measure out cookie dough. Press 1 or 2 large pieces of semi-sweet chocolate into the top of each cookie, then transfer to the prepared baking sheet leaving a couple inches in between each. I bake 6 cookies at a time.
Bake the cookies. Bake for 11-12 minutes, or until the edges are golden brown. The centers may look slightly underbaked, but this is okay! Sprinkle each cookie immediately with a pinch of flaky sea salt. Cool slightly for about 5 minutes, then use a spatula to transfer the cookies to a cooling rack. Repeat with remaining cookie dough. Enjoy!