Beat the granulated sugar, 8 tablespoons (113g) of butter, vanilla extract, and salt in a large bowl on medium speed for 2 to 3 minutes until smooth. Add the egg yolk and mix to combine.
Add the flour and 1/2 cup (42g) of cocoa powder to the bowl. Mix on low speed just until a dough forms and no dry spots remain.
Divide the dough into 24 even pieces. Roll each into a ball and place them into a lightly greased 24-cup mini muffin pan. Press the center of each ball with a floured rounded teaspoon measuring spoon to form a cup shape, pushing the dough up the sides. Chill the pan in the refrigerator for 20 minutes.
Preheat the oven to 375°F (190°C). Bake the chilled cookie cups for 14 to 18 minutes until the edges are firm and the internal temperature reaches 160°F (71°C) for egg safety. Remove from the oven and carefully press the centers again to reinforce the cup shape. Let cool completely in the pan.
Melt the 1/4 cup (40g) of chopped chocolate in a small microwave-safe bowl in 30-second intervals. Remove the cooled cookie cups from the pan. Carefully cut each pretzel in half down the center to create handle shapes.
Dip the cut ends of the pretzel handles into the melted chocolate and press them against the sides of the cookie cups. Place the cups upside down on a parchment-lined baking sheet so the handles can dry without sliding. Let the chocolate set completely, about 2 hours.
Place the 2/3 cup (113g) of chopped chocolate and 2 tablespoons (28g) of butter in a heat-proof measuring cup. Warm the heavy cream in a small saucepan until it steams, then pour it over the chocolate and butter. Let sit for 3 minutes, then stir until smooth.
Turn the cookie cups right side up. Spoon about 2 tablespoons of the ganache into each cup. Top each with three mini marshmallows. Let the ganache set for 1 hour at room temperature.
Dust the tops with cocoa powder just before serving.