Place the butter in a light-colored saucepan over medium heat. Whisk constantly as the butter melts, foams, and eventually browns. Once it reaches a deep amber color and smells nutty, immediately transfer it and all browned bits into a heat-proof bowl. Let cool for 30 minutes until room temperature but still liquid.

In a medium bowl, whisk together the all-purpose flour, bread flour, baking soda, baking powder, and fine sea salt until aerated and combined.

In a large mixing bowl, combine the cooled browned butter with the dark brown sugar and granulated sugar. Whisk vigorously by hand or with a mixer until the mixture is smooth and no sugar clumps remain.

Add the whole eggs, egg yolk, and vanilla. Beat on medium-high speed for approximately 2 minutes until the mixture significantly lightens in color, thickens, and becomes glossy.

Add the dry ingredient mixture to the wet ingredients. Use a silicone spatula to fold the dough until just a few streaks of flour remain; do not overwork the gluten.

Fold in the chopped chocolate chunks, ensuring the smaller chocolate 'shards' are included to create a marbled effect.

Cover the dough tightly with plastic wrap and refrigerate for a minimum of 2 hours, though 24-48 hours is recommended for maximum flavor development and enzyme breakdown.

Preheat the oven to 350°F (175°C). Line two large heavy-duty baking sheets with parchment paper or silicone mats.

Scoop approximately 3 tablespoons of dough (60g) per cookie. Space the dough balls 3 inches apart on the prepared sheets.

Bake for 10 to 12 minutes. The edges should be golden-brown and set, while the centers should remain slightly pale and soft.

Immediately upon removal from the oven, sprinkle each cookie with a pinch of flaky sea salt. Allow cookies to cool on the baking sheet for 10 minutes to finish setting before transferring to a wire rack.