Preheat the oven to 400°F.
Add the brown sugar and white sugar to the stand mixer with the cooled brown butter, beat until well combined.
One at a time add the eggs, yolk and vanilla allowing to beat well between additions. Beat on high speed until the mixture is creamy and resemble frosting.
Stop the mixer and sprinkle with both kinds of flour, baking soda, baking powder, 1 teaspoon salt, and chocolate chunks. Stir until just combined, making sure to scrape the bottom of the bowl to insure the mixture is well combined.
Scoop onto a cookie sheet that has been covered with parchment, leaving enough space for the cookies to spread. Sprinkle with flakey salt.
Bake for 9 minutes or until the cookies are golden brown at the edges and the center has puffed. Pull the parchment onto the counter to allow the cookies to cool.