For the cupcakes: Position an oven rack in the center of the oven, and preheat to 350 degrees F. Line a 12-cup muffin tin with cupcake liners, and lightly coat with cooking spray.
Whisk together the flour, baking soda, salt and baking powder in a medium bowl; set aside.
Bring the cocoa powder, milk and 1/2 cup water to a simmer in a small saucepan over medium heat, and whisk until the cocoa dissolves into a smooth, thicker mixture, about 3 minutes. Stir in the vanilla, and set aside until just slightly warm to the touch.
Beat the butter and sugar on medium-high speed with an electric mixer until combined and fluffy, about 3 minutes. Add the eggs and egg yolks one at a time, beating to incorporate after each addition. Continue to beat while slowly pouring the cocoa mixture into the bowl (be sure to scrape out any cocoa that coats the saucepan) just until incorporated, scraping down the side of the bowl as needed. Reduce the speed to medium, add the flour mixture and beat until just incorporated. Finish stirring by hand to avoid overmixing.
Divide the batter evenly among the lined muffin cups, and bake until the cupcakes bounce back when gently pressed and a toothpick inserted in the center comes out clean, 18 to 20 minutes. Let them cool in the pan for a few minutes, then transfer to a rack to cool completely. Unwrap each cupcake, and use a small knife to cut out a small "plug" of cake in the middle of each bottom, cutting about halfway through the cupcake.
For the filling: Beat the marshmallow, confectioners' sugar and butter with an electric mixer in a medium bowl until smooth. Transfer the mixture to a large resealable plastic bag, and snip off one corner. Pipe the filling into the holes cut out of the cupcakes; use the plugs or scraps of the cake you removed to plug the holes back up.
For the glaze: Combine the butter, chocolate, honey and salt in a small microwave-safe bowl, cover with plastic wrap and poke a hole in it to vent. Microwave on high (at 100 percent power) for about 1 minute, until the butter and most of the chocolate is melted. Whisk until smooth; let cool, 15 to 20 minutes. Dip the top of each cupcake in the glaze, and let it set up, about 30 minutes.
For the icing: Put the filled and glazed cupcakes on a rack set over a baking sheet or piece of parchment. Whisk the confectioners' sugar, butter and 2 tablespoons water together in a small bowl. Top each cupcake with a drizzle of icing; let harden, about 10 minutes. Put the finished cupcakes in fresh liners. The cupcakes can be baked, filled, glazed and iced a day ahead and stored in an airtight container at room temperature.
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