In a medium mixing bowl, whisk together the flour, baking soda, and salt until evenly combined. Set aside. In a separate large bowl—or the bowl of a stand mixer—add the softened butter, both sugars, and vanilla extract. Using the creaming method, mix vigorously by hand with a wide rubber spatula, pressing and smearing the butter into the sugars until the mixture becomes smooth and slightly fluffy. Alternatively, you can use a hand mixer, or a stand mixer fitted with the paddle attachment on medium-low speed for 1–2 minutes. The texture should resemble a thick paste or damp sand, not a light or overly aerated mixture. Stir in the honey, then mix in the egg until fully incorporated and smooth.

Next, add the dry ingredients (the flour mixture) into the wet ingredients all at once. Stir gently until most of the flour is absorbed. Before the dough is fully combined, fold in the chopped chocolate chunks, continuing to stir just until everything is evenly mixed. The dough should be soft and slightly moist, but not sticky.

Cover the surface of the dough directly with plastic wrap and refrigerate for at least 8 hours and up to 24 hours for the best flavor and texture. This rest period allows the ingredients to meld and the dough to firm up. If you're in a hurry, you can bake the cookies after 4 hours of chilling, though for ideal results, 8 hours is strongly recommended.

When you're ready to bake, preheat the oven to 350°F (175°C) and line two large baking sheets with parchment paper. Scoop the chilled dough using a 1 ½-ounce cookie scoop and roll each portion into a smooth ball. If the dough feels too firm after refrigeration, let it sit at room temperature for 20–30 minutes until it's easier to work with. If you don’t have a scoop, simply divide the dough into 16 equal portions. Arrange the dough balls on the prepared baking sheets, leaving about 2 inches of space between each. Do not flatten them before baking.

Note: For slightly smaller cookies, divide the dough into 18 portions and reduce the baking time by 1–2 minutes.

For an extra bakery-style touch, press a few additional chocolate chunks on top of each dough ball before baking. Bake six cookies per sheet for 9–11 minutes, or until the cookies are puffed, lightly golden around the edges, and still soft in the center. Avoid overbaking—they will continue to set up on the hot baking sheet after coming out of the oven. If baking the smaller cookies, check for doneness at 8–10 minutes. Once out of the oven, let the cookies rest on the baking sheets for 2 minutes before carefully transferring them to a wire rack to cool completely. While the cookies are still warm, sprinkle with flaky sea salt if desired for a final touch.