1. Place the pudding mix and milk in a 2-quart saucepan over medium-high heat. Whisk constantly until the mixture comes to a boil and thickens, 4 to 5 minutes. Remove pan from heat, add the chocolate chips, butter, and vanilla; stir until melted, 2 minutes. Cover pudding with plastic wrap placed directly on its surface and let cool to room temperature, 45 minutes.
2. Blend cake mix, cocoa powder, buttermilk, oil, eggs, and vanilla in a large bowl with a mixer set on low speed for 30 seconds. Stop mixer and scrape down the sides of the bowl with a rubber spatula. Increase mixer speed to medium and beat 2 minutes more, scraping down sides again, if needed (batter should be thick and well combined). Spoon a heaping 1/4 cup into each cup, filling two-thirds of the way.
3. Bake in middle of oven until cupcakes are golden and spring back when lightly pressed, 17 to 20 minutes (you can also bake cupcakes in upper and lower thirds of oven, switching position of pans halfway through). Let cupcakes cool in pans on racks, 5 minutes. Remove 4 cupcakes from the pan, discarding paper, and crumble them into a bowl to make coarse crumbs. Remove remaining cupcakes from pans and place on racks to cool for 15 minutes before filling.
4. Divide filling/frosting into two portions. Fit a pastry bag with a large round tip and spoon 1 cup of the filling portion into bag. Gently push the tip into the center of each cupcake and squirt a generous amount of pudding inside. Refill the bag as needed and repeat with remaining cupcakes.
5. Dollop a heaping tablespoon pudding from remaining portion on each cupcake, spreading slightly, then dollop a spoonful of whipped cream on top of pudding. Sprinkle cupcake crumbs over top. Garnish with a cherry. Repeat with remaining cupcakes. Makes 20 cupcakes.