Begin by setting up a double boiler over gently simmering water. Place a heatproof bowl on top and add the cubed unsalted butter along with half of the dark chocolate chips. Stir continuously until the mixture melts and becomes smooth, then remove it from heat and let it cool slightly.

In a stand mixer, combine the room-temperature eggs, dark brown sugar, and granulated sugar. Beat the mixture on medium-high speed for approximately 4 to 5 minutes until pale, thick, and resembling a ribbon-like consistency.

Reduce the mixer speed to low. Gradually stream in the cooled melted chocolate mixture along with the pure vanilla extract. Mix just until combined, being careful not to overmix.

In a separate bowl, whisk together the gluten-free flour, sifted cocoa powder, and baking powder. Sift this dry mixture over the wet ingredients, and gently fold everything together using a rubber spatula until no streaks of flour are visible.

Cover the bowl tightly with plastic wrap and refrigerate for at least 45 minutes.

Preheat your oven to 350°F (175°C). Once the dough has chilled, use a scoop to portion out 3-tablespoon mounds of dough onto a parchment-lined baking sheet, leaving about 2 inches of space between each mound.

Bake the cookies for 10 to 12 minutes. The edges should appear set, while the centers remain soft. Press the remaining dark chocolate chips into the tops of the warm cookies and sprinkle with coarse sea salt flakes.

Allow the cookies to rest on the baking sheet for 10 minutes before transferring them to a wire rack to cool completely.