Line a large baking sheet with parchment paper and set aside.
In a medium bowl, whisk together the 2½ cups all-purpose flour, 2 tablespoons malted milk powder, 1 teaspoon baking soda, and 1 teaspoon fine sea salt and set aside.
Slice 1 cup salted butter (use cold for best results) into tablespoons and cream with ¾ cup granulated sugar, ¾ cup dark brown sugar, and 1 teaspoon vanilla extract in a stand mixer fitted with a paddle attachment at speed 4 for 3 minutes, scraping down the sides of the bowl after each minute.
Mix in the 2 large eggs until fully combined.
Gradually add in the flour mixture and mix until fully combined.
Fold in most of the chopped 12 ounces semi-sweet chocolate and 1 cup chopped walnuts (if using).
Use a medium cookie scoop (1.5 tablespoons) to scoop the cookie dough into 1-ounce portions and place the scoop on the prepared baking sheet. Then, gently press another scoop of dough into the top of the first so they are stacked.
Top the scoops of dough with the remaining chopped chocolate and sprinkle with flaky sea salt.
Chill the dough for at least 3 hours before baking for best results.
When ready to bake, preheat the oven to 350°F and line another large baking pan with parchment paper
Place 6 of the chilled cookie dough balls at least 3 inches apart on the baking pan. Bake for 9 to 12 minutes or until the edges are golden brown and the centers have lost most of their glossiness (they will still be gooey in the center when you pull them out and will continue cooking on the pan).
As soon as the cookies come out of the oven, gently press a few of the ½ cup semi-sweet chocolate chips into the tops of each one while they are still on the pan. This is optional if you really want that classic chocolate chip cookie look.
Allow the cookies to cool on pan for 2 to 3 minutes before transferring to a cooling rack.
Repeat with the next 6 cookies, either using another pan or chilling the pan from the first batch in the fridge for a few minutes.
Cookies will be crisp on the edges and gooey in the center when fresh out of the oven. After cooling and resting, the centers will become more chewy and less gooey.