In a medium bowl, whisk together the 2¼ cups bread flour, 2 tablespoons finely ground espresso or coffee, 2 tablespoons malted milk powder, 2 tablespoons corn starch, and ½ teaspoon baking soda.
In the bowl of a stand mixer fitted with a paddle attachment, cream together 1 cup light brown sugar, ¾ cup salted butter, ½ cup granulated sugar, 1 tablespoon vanilla bean paste, and 1 teaspoon salt until smooth. 1 min on 2 and 1 min on 4 speed.
Add in 1 large egg and 1 additional large egg yolk and beat until light and creamy. About 5 minutes, scraping down the sides of the bowl halfway through.
Add the dry ingredients to the wet ingredients a little at a time, mixing between each addition.
Fold in about 1½ cups of the 2 cups dark chocolate chips. Reserving the rest for topping.
Measure the dough into balls, using a #20 cookie scoop, about 2.5 ounces each. Press the reserved chocolate chips into the top of the dough.
Chill uncovered in the fridge for at least 2 hours preferably overnight.
Preheat oven to 350°F and place balls on a parchment-lined cookie sheet at least 3 inches apart. Sprinkle with flaky sea salt if desired, and bake for 12 to 15 minutes until the edges are golden brown. Let the cookies cool on the pan for a few minutes before transferring to a wire rack. Chill the baking pan in the freezer for a couple of minutes between baking batches so you don't put cookie dough on a hot pan.