Brown the butter. Melt 140 grams of butter in a medium skillet over medium heat. Stir continuously with a rubber spatula until it transforms into a rich amber color and gives off a nutty aroma. This means it's done! Take the pan off the heat right away and turn off the burner.
Let the butter cool. Pour the browned butter into a large bowl or the bowl of a stand mixer with a whisk attachment. Make sure to scrape all those tasty, toasted bits from the bottom of the pan into the bowl. You should have about 116 grams of browned butter. Let it cool in the bowl at room temperature for 30 minutes.
Whisk in the sugars. Combine the sugar and dark brown sugar with the cooled butter. Whisk for 30 seconds on medium speed until they're well combined; the mixture should resemble wet sand.
Cream together the wet ingredients. Add the large egg, egg yolk, and vanilla extract to the bowl. Whisk until the mixture is just combined, smooth, and creamy. Be careful not to overmix it.
Add the dry ingredients. On low speed, add the gluten-free flour, almond flour, baking soda, and salt. Mix until just combined, with a few flour streaks remaining.
Add the chocolate. Using a rubber spatula, fold in the chopped chocolate and chocolate chips until they're evenly distributed throughout. Cover the bowl and refrigerate the dough for 2 hours. (If chilling longer than 2 hours, let the dough come to room temperature for 30-45 minutes before baking).
Scoop and roll the dough. Preheat your oven to 350°F. Line two large baking sheets with parchment paper. Using a large, 2-tablespoon cookie scoop or a spoon, portion the cookie dough into 40-gram balls, ideally weighed on a food scale for accuracy. Roll each ball of dough smooth between your palms. Place 5 of these smooth dough balls onto each prepared baking sheet, ensuring they're spaced apart.
Bake the cookies. Place the baking tray in the oven and bake for 8-10 minutes until golden on top, browned around the edges, and soft in the middle.
Add the flaky sea salt. Once you remove the baking sheet from the oven, immediately sprinkle the tops of the cookies with flaky sea salt. If you want perfectly round cookies, use a large cookie cutter to gently shape them while they're still warm. Let the cookies rest on the baking sheet for 2-3 minutes before carefully transferring them to a wire rack to finish cooling.