Preheat oven to 325 degrees. Whisk together flour, cocoa powder, baking soda, and salt in a medium bowl; set aside. Melt chocolate and butter in a heatproof mixer bowl set over a pan of simmering water. Attach bowl to mixer fitted with the paddle attachment. Add sugar, extracts, and eggs; mix on medium-low speed until combined. Reduce speed to low; mix in flour mixture. Stir in one-third of the candies. Refrigerate dough until firm, about 30 minutes (or wrap in plastic and refrigerate overnight).
Using a 1 1/2-inch ice cream scoop, form mounds of dough; dip tops into remaining candies to coat. Place cookies, candy sides up, on baking sheets lined with parchment paper, spacing 2 inches apart. Bake cookies until just set, about 15 minutes. Let cool on sheets on wire racks. Cookies can be stored in an airtight container at room temperature up to 3 days.