Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper.
In a medium bowl, whisk together 1¾ cups flour, 1 cup malted milk powder, ¼ cup unsweetened cocoa powder, 1½ teaspoons baking powder, and ¼ teaspoon salt. Set aside.
In the bowl of a stand mixer fitted with the paddle (or in a large bowl with an electric mixer), beat 11 tablespoons unsalted butter and ⅔ cup sugar on medium speed until very smooth, about 2–3 minutes.
Add the 2 eggs one at a time, mixing until each is incorporated. Beat in 1 teaspoon vanilla extract. The mixture may look slightly curdled—this is normal.
Reduce mixer speed to low. Add half of the dry ingredients and mix just until they disappear into the batter (do not overmix).
With the mixer still on low, add ¼ cup whole milk and mix until combined.
Add the remaining dry ingredients and mix on low only until just incorporated. Scrape the bowl with a spatula as needed.
Fold in 2 cups coarsely chopped whoppers and 1 cup semi-sweet chocolate chips with a spatula until evenly distributed. If you want to garnish the cookies, set aside a few extra whoppers for topping.
Drop the dough by rounded tablespoons onto the prepared baking sheets, spacing cookies about 2 inches apart.
Bake one sheet at a time (or both if your oven allows even baking) for 11–13 minutes, until the edges are set and the centers are still slightly soft.
If desired, immediately press a few reserved whoppers into the hot cookies to garnish. Let cookies cool on the baking sheet for about 5 minutes, then transfer to a wire rack to cool completely.