Place an oven rack in the center position and preheat the oven to 350°F (175°C). Spray every cup of your mini muffin pan generously with nonstick baking spray, including the rims. Set out eggs and milk about 30 minutes ahead so they come to room temperature.
In a medium bowl, whisk 1 1/2 cups all-purpose flour, 1 1/2 teaspoons baking powder, and 1/4 teaspoon salt for about 30 seconds. Set aside.
In a large bowl, beat 1/2 cup softened unsalted butter and 3/4 cup granulated sugar with a hand mixer on medium-high speed for 2 to 3 minutes until pale and fluffy. Scrape down the sides halfway through.
Add the 2 room temperature eggs one at a time, beating for about 30 seconds after each. Pour in 2 teaspoons vanilla extract and mix until smooth and creamy.
Add about one third of the flour mixture and mix on low speed until just combined. Pour in half of the 1/2 cup whole milk, then add another third of the flour mixture. Add the remaining milk and finish with the last of the flour, mixing only until no dry streaks remain.
Use a spoon or small cookie scoop to add a heaping tablespoon of batter to each prepared cup, filling it about two thirds full. Bake for 10 to 12 minutes, until tops spring back when touched and a toothpick comes out clean. Bake remaining batter in a second batch.
Let the bites rest in the pan for 5 minutes, then run a small knife around each edge and lift them out. Transfer to a wire cooling rack and cool for at least 30 minutes before filling.
In a medium bowl, whisk 3 egg yolks, 1/4 cup sugar, 2 tablespoons cornstarch, and 1/8 teaspoon salt with 2 tablespoons of the 1 cup milk until smooth. Heat the rest of the milk in a saucepan until steaming. Slowly pour half the hot milk into the yolk mixture while whisking constantly. Return everything to the saucepan and cook over medium heat, whisking nonstop, for 2 to 3 minutes until thickened. Keep whisking for one more minute, then remove from heat.
Whisk in 1 tablespoon butter and 1 teaspoon vanilla extract until glossy. Pour through a fine mesh strainer into a clean bowl. Press plastic wrap directly onto the surface and refrigerate for at least 2 hours until completely cold and thick.
Add 1 cup semi-sweet chocolate chips to a small heatproof bowl. Heat 3/4 cup heavy cream until it just begins to simmer. Pour over the chocolate chips and let sit for 2 minutes. Whisk slowly from the center outward until smooth and shiny. Let cool for 10 to 15 minutes until thickened but still spoonable.
Use a serrated knife to slice each cake bite in half horizontally. Pipe about 1 teaspoon of cold pastry cream onto each bottom half, then gently set the top half back in place.
Dip the top of each filled bite into the ganache, or spoon about a teaspoon over the top and let it drip down the sides. Place on a parchment-lined tray and refrigerate for 15 to 20 minutes so the ganache sets. Serve chilled or cool.