To make the pastry cream, whisk milk and 1/4 cup sugar together in a large saucepan.
Bring to a boil over medium heat, whisking regularly.
In a medium bowl, whisk together the egg yolks and egg.
Whisk the remaining sugar and cornstarch into the eggs.
Once the milk comes to a boil, slowly stream it into the egg mixture while whisking constantly so that you do not cook the eggs.
Pour the mixture back into the saucepan, and slowly bring to a boil, whisking constantly.
Once the mixture comes to a boil, continue to cook until it thickens.
Remove from the heat, and whisk in the butter and vanilla.
Pour into a heat-proof container, and press a piece of plastic wrap directly on the surface to prevent a skin from forming.
Refrigerate until chilled before using.
To make the cupcakes, preheat the oven to 325 F. Line 12 muffin tins with cupcake liners. Set aside.
Whisk the flour, cocoa powder, baking powder, baking soda, and salt together in a large bowl until well-combined. Set aside.
In a medium bowl, whisk together eggs, sugars, oil, and vanilla together until well-combined.
Whisk the wet ingredients into the dry ingredients.
Add the buttermilk and whisk until just incorporated. The batter will be thin.
Divide the batter among the prepared muffin tins, filling each tin half full.
Bake for 15-20 minutes, or until a toothpick inserted in the center comes out clean.
Remove from pan and let cool to room temperature on a wire cooling rack.
To make the ganache, add the chocolate to a heat-proof bowl.
Heat the cream until it simmers.
Pour the cream over the chocolate, and cover.
Let the mixture sit for 5 minutes without stirring.
Uncover, and whisk until smooth and well-combined.
To put it all together, cut top off of cupcake (the domed muffin top).
Using a small (1 tablespoon) cookie scoop, scoop out a piece of cake. Discard, eat, or otherwise use the cake.
Using the cookie scoop, scoop out a scoop of pastry cream, and place it in the hollowed out portion of the cupcake.
Replace top of the cupcake, gently pressing the top onto the cream.
Top cupcake with some chocolate ganache.