Cream butter and sugar together in a large bowl until light and fluffy, about 3-4 minutes. Beat in eggs one at a time, then add vanilla extract.
In a separate bowl, whisk together flour, baking powder, and salt. Gradually add to butter mixture, mixing on low until just combined. Dough will be thick and slightly sticky.
Preheat oven to 350°F. Spray a mini muffin pan with nonstick cooking spray. Roll dough into 1-inch balls and place in muffin cups. Press down and up sides to form cups.
Bake for 10-12 minutes until edges are lightly golden. Centers may look slightly underdone. Cool in pan 5 minutes, then transfer to wire rack. Press centers down if they puffed up.
Make custard: Whisk egg yolks in medium bowl. In saucepan, combine milk, 3/4 cup sugar, and cornstarch. Cook over medium heat, stirring constantly, until thickened and bubbling, 5-7 minutes.
Remove from heat. Temper egg yolks by slowly whisking in half the hot milk mixture. Pour egg mixture back into saucepan. Cook 1 more minute, stirring constantly.
Remove from heat. Stir in 2 tablespoons butter and 1 teaspoon vanilla. Transfer to bowl, cover with plastic wrap pressed onto surface. Refrigerate until cold, about 30 minutes.
Make ganache: Place chocolate chips in heatproof bowl. Heat cream and 2 tablespoons butter in saucepan until butter melts and cream simmers. Pour over chocolate, let sit 2 minutes, stir until smooth.
Assemble cookie cups: Spoon or pipe chilled custard into cooled cookie cups, filling almost to top. Drizzle chocolate ganache over each. Let sit 10 minutes before serving.