Preheat the oven according to the cake mix package directions and line a cupcake pan with cupcake liners.
In a large mixing bowl, combine the chocolate fudge cake mix, pudding mix, whole milk, melted butter, eggs, egg yolk, vanilla extract, and espresso powder. Mix until smooth and fully combined.
Fill each cupcake liner about 2/3 of the way full. Bake according to the package directions, or until the cupcakes spring back lightly when touched and a toothpick inserted into the center comes out clean.
Let the cupcakes cool completely before frosting.
To make the frosting, beat the softened butter and peanut butter together until smooth and creamy. Add the powdered sugar, vanilla extract, and 2 tablespoons of milk. Beat until fluffy, adding the remaining tablespoon of milk only if needed.
Pipe or spread the peanut butter frosting onto the cooled cupcakes.
Top each cupcake with mini chocolate chip cookies, mini pretzels, and mini chocolate chips.
Finish with a pinch of flaky sea salt and Father’s Day toppers.