Preheat oven to 350°F (175°C). Line two 12‑cup muffin tins with liners and lightly spray.
In a bowl, sift flour, cocoa, baking soda, baking powder, and salt. Set aside.
Melt butter and chopped chocolate together; set aside to cool slightly.
In a large bowl, beat sugars, eggs, egg yolk, and vanilla until smooth. Add melted chocolate mixture and stir to combine.
Gently fold in flour mixture in three parts, alternating with sour cream, beginning and ending with flour. Don’t overmix.
Pour in hot water (or coffee) and stir until just combined. Batter will be thin.
Fill each cupcake liner about ⅓ full, push a peanut butter cup in the center, then top with more batter to fill about ⅔.
Bake 16–18 minutes or until toothbrush tester comes out with moist crumbs, not wet batter. Let cool completely.
For frosting: beat butter until smooth, add vanilla. On low speed, gradually add confectioners’ sugar. Add milk, salt, and peanut butter; beat on medium-high until light and fluffy.
For ganache: heat cream until near boiling, pour over chopped chocolate + peanut butter; sit 1–2 minutes, then stir until smooth. Let cool slightly before using.
Pipe frosting on cooled cupcakes. Drizzle (or spoon) ganache over frosting if using. Garnish with peanuts or mini cups.
Serve. Store at room temperature or in fridge (depending on climate).