Preheat the oven to 350ºF and prepare 1-2 large baking sheets with parchment paper.
In a large bowl, whisk together the melted brown butter, sugars, vanilla extract, egg, and yolk until smooth. Add the gluten-free flour, baking powder, baking soda, and salt to the same bowl. Use a rubber spatula to gently mix together the dry ingredients, then fold into the wet ingredients to create the dough. Finally, fold in the chocolate chunks, saving some to top the cookies with before baking.
Use a 3 tablespoon scoop or an ice cream scoop to form the dough into 10 balls. You can bake the cookies immediately to be slightly crispier, or place the dough balls on a plate and refrigerate for 30 minutes for chewier cookies.
Place the cookie dough balls the baking sheet(s) with enough room to spread. Press some extra chocolate into the tops. Bake for 10-12 minutes, until lightly golden. The middles will still look soft. I do about 11 minutes.
Wearing oven mitts, slam the baking sheet on the counter a few times to encourage the cookies to spread. Immediately take a large cookie cutter or a glass and gently swirl it around each cookie to create the perfect circle shape.
Allow the cookies to cool on the baking sheet for 15 minutes until they are set, then transfer to a wire rack to continue cooling. Sprinkle with flaky sea salt. Enjoy warm or allow to come to room temperature.