Position an oven rack in the center of the oven and preheat the oven to 350ºF. Generously coat the top of the muffin pans with baking spray. Line 20 of the muffin cups with paper baking cup liners. Set aside.
To make the cream cheese filling, place the cream cheese, egg yolk, and vanilla extract in the bowl mixer fitted with the flat beater. Beat the cream cheese mixture until mixture is smooth and fluffy, about 2 minutes. Transfer the mixture to a small bowl and set aside. Wash and dry the mixer bowl, place back on the mixer, and fit the mixer with the whip attachment.
To make the cupcakes: Mix the flour, sugar, cocoa powder, espresso powder, baking soda, baking powder.
In a medium bowl, whisk eggs, and then whisk in the sour cream, buttermilk, canola oil, and vanilla extract.
With the mixer on medium-low, sift the dry ingredients into the mixer bowl. Once all the dry ingredients are sifted in, slowly pour in the sour cream mixture, mixing just until the flour disappears. Now, pour the boiling water down the side of the bowl, mixing just until incorporated. Turn the mixer off. Remove the mixer bowl, and use a rubber spatula to blend in any flour remaining on the sides or bottom of the bowl.
To fill the cupcakes, spoon 2 tablespoons of cupcake batter into each lined baking cup. Then spoon about 2 teaspoons of the cream cheese filling on top and in the center of the batter. Finish by adding another tablespoon of batter on top of each cupcake, covering the cream cheese filling. Bake cupcakes in the center of the oven until the tops crown, and a toothpick inserted along the edge comes out clean, 16 to 20 minutes. (If you insert the toothpick in the center you’ll hit the soft cream cheese, which won’t be a good indicator of doneness.) For even baking, at the midpoint, rotate the pans from front to back. Cool the cupcakes in the pans set on wire racks for 10 minutes. Lift out the cupcakes and set them on wire racks to cool completely.