Prepare the Banana Cream Filling: Stir together banana and lemon juice in a small bowl. Beat 1/4 cup powdered sugar, 3 ounces cream cheese, and 2 tablespoons heavy cream in a medium bowl with an electric mixer at low speed until smooth. Stir in 1/2 cup of the banana-lemon mixture, reserving the remaining 3/4 cup banana-lemon mixture for the batter.
Prepare the Cupcakes: Preheat oven to 350°F. Place baking cup liners in a 12-cup muffin pan; lightly coat liners with cooking spray. Whisk together flour, baking powder, baking soda, nutmeg, and 1/4 teaspoon salt in a bowl. Beat granulated sugar, brown sugar, and 1/2 cup butter at medium speed in a large bowl until well combined, about 3 minutes. Add milk, eggs, and 1/2 teaspoon vanilla; beat at low speed until combined, about 2 minutes. (Mixture may look curdled.) Gradually add flour mixture, beating at medium-low speed until smooth, about 3 minutes. Stir reserved 3/4 cup banana-lemon mixture into batter.
Spoon about 1 tablespoon cupcake batter into each muffin cup; top evenly with Banana Cream Filling. Top evenly with remaining cupcake batter, and bake in preheated oven until tops are golden brown and cupcakes spring back when lightly touched, 18 to 20 minutes. Cool in pan 5 minutes. Remove cupcakes to a wire rack, and cool completely, about 30 minutes.
Prepare the Peanut Butter Buttercream: Beat peanut butter, 1/4 cup butter, 3 tablespoons cream cheese, 1/4 teaspoon vanilla, and 1/8 teaspoon salt in a medium bowl at medium-low speed until smooth, about 2 minutes. Add 3 cups powdered sugar alternately with 3 tablespoons of the cream, beating at low speed until smooth after each addition. Add the remaining 1 tablespoon of the cream, 1 teaspoon at a time, if needed, to reach desired consistency. Spoon frosting into a ziplock plastic freezer bag. Snip 1 corner of bag to make a small hole. Pipe about 3 tablespoons buttercream onto each cupcake. Drizzle melted chocolate evenly over buttercream.