Preheat the oven to 350°F and line a large baking sheet with parchment paper and set aside. If you only have a 9x13-inch baking sheet, you'll want to use two baking sheets for two batches.
In a medium bowl, whisk together 2 cups all-purpose flour, ½ cup Dutch cocoa powder, 2 tablespoons black cocoa powder, 2 tablespoons cornstarch, 2 tablespoons powdered milk, and ¼ teaspoon baking soda. Set aside.
Add together 1 cup granulated sugar, ½ cup salted butter, and ½ teaspoon salt to a large bowl or stand mixer fitted with a paddle attachment and cream for 1 minute.
Add in 1 large egg and beat until combined. Beat in 1 additional large egg yolk, 2 ounces whole milk, and 1½ teaspoons pure vanilla extract and mix just until combined.
Add half of the dry ingredients to the wet ingredients and beat just until incorporated. Then add the remaining dry ingredients and mix until thoroughly combined.
In a separate medium bowl, beat together 6 ounces cream cheese, 1 cup powdered sugar, and 1 teaspoon vanilla bean paste until smooth.
Scoop the dough with a #24 cookie scoop into 16 1.8-ounce portions. Gently press the dough flat and then shape it into a bowl shape.
Place a heaping teaspoon of the cream cheese mixture (about .3 ounces) in the well. There may be some filling leftover.
Then, gently use your hands to fold and work the dough up and around the sides and top of the cheesecake mixture.
Pat and pinch the dough to seal it and roll it between your palms to make a smooth ball.
Place the cookies on the baking sheet, usually with the sealed side down. Place cookie dough at least 2 inches apart for regular cookies or 4 inches apart for large cookies on the prepared baking sheet.
Bake for 9 to 11 minutes for regular cookies until the edges are just set, and the top has a matte look with some slight cracking. The cookies will look slightly underdone; this is normal, as they will continue to cook as they cool.
Allow the cookies to cool on the pan for 15 minutes before transferring them to a wire rack with a spatula to cool completely. These cookies are very soft right after baking and will firm up while they cool.
Once cooled, melt the ½ cup chocolate melting wafers in the microwave at 30-second intervals, stirring between each one until fully melted.
Transfer the melted chocolate to a piping bag, drizzle it over the cookies, and let set until it has hardened.