Brown the butter. Melt butter in a light-colored saucepan over medium heat. Cook, stirring frequently, until milk solids turn golden brown and smell nutty, about 4-6 minutes. Remove from heat and cool for 10-15 minutes.
Mix dry ingredients. In a medium bowl, whisk together flour, baking soda, and kosher salt.
Mix wet ingredients. In a large bowl, whisk browned butter, brown sugar, and granulated sugar until smooth. Add egg, egg yolk, and vanilla and whisk until fully combined.
Combine. Add dry ingredients to wet and stir until just combined. Do not overmix.
Add chocolate. Fold in chocolate chips and chopped chocolate.
Chill. Cover and refrigerate dough for 30 minutes.
Prep. Preheat oven to 350 degrees F. Line two baking sheets with parchment paper.
Portion. Scoop dough into 2-tablespoon portions and place 2 inches apart on prepared baking sheets.
Bake. Bake for 10-12 minutes, until edges are lightly golden but centers still look slightly underbaked.
Finish. Immediately sprinkle each cookie with a small pinch of flaky sea salt.
Cool. Rest cookies on the baking sheet for 5 minutes, then transfer to a wire rack.