Preheat the oven to 350°F. Line two 12-cup muffin tins with cupcake liners.
In a medium bowl, whisk together 1 1/3 cups all-purpose flour, 1 1/4 teaspoons baking soda, and 1/4 teaspoon salt. Set aside.
In a large bowl, whisk 1 large egg until combined. Add 3/4 cup loosely packed brown sugar and whisk until smooth. Stir in 1 teaspoon vanilla extract, 1/4 cup Greek yogurt, and 1/2 cup melted butter until evenly combined.
Add the dry flour mixture to the wet ingredients and stir until mostly combined. Fold in 3 cups mashed ripe bananas and 1/3 cup milk, mixing until the batter comes together. Stir in 1 cup chocolate chips. Set the cupcake batter aside.
Make the brownie batter: in a large bowl, stir together 1/2 cup melted butter and 4 tablespoons cocoa powder until smooth.
In a separate bowl, beat 2 eggs. Add 1/2 cup sugar and 1/2 teaspoon vanilla extract to the eggs and beat until combined. Stir this egg-sugar mixture into the butter-cocoa mixture.
Add 3/4 cup all-purpose flour and 1/4 teaspoon salt to the brownie mixture and mix until just combined. Stir in 1/2 cup chocolate chips.
Assemble the cupcakes: spoon about 1/8 cup of the banana batter into the bottom of each lined cup so each liner is about 1/4 full. Spoon about 1 tablespoon of brownie batter into the center of each cup (keep the brownie batter centered). Top each with enough banana batter to bring the liners to about 3/4 full, covering the brownie filling.
Bake the cupcakes for 15–18 minutes, until a toothpick inserted into the banana portion (avoiding the brownie center) comes out with a few moist crumbs but not wet batter. Remove from the oven and let the cupcakes cool in the pan for about 5 minutes, then transfer to a wire rack to cool completely.
Make the meringue: set a pot with about 2 inches of simmering water over medium-low heat. In a heatproof bowl, whisk together 4 large egg whites, 1 1/2 cups granulated sugar, 1/2 cup light corn syrup, and a large pinch of salt until grainy.
Place the heatproof bowl over the simmering water (double boiler) and whisk constantly until the sugar has dissolved and the mixture is warm, about 5 minutes. Be careful not to let the bowl get so hot that the eggs begin to cook.
Transfer the warmed egg-white mixture to the bowl of a stand mixer fitted with the whisk attachment (or use a hand mixer). Beat on high until the meringue forms stiff, glossy peaks, about 5 minutes. Beat in 2 teaspoons pure vanilla extract. Cover the meringue until ready to use.
Frost each cooled cupcake with a large dollop of the meringue (or pipe if you prefer) and smooth or shape as desired.
Toast the meringue: turn on the oven broiler. Place up to 12 frosted cupcakes on a baking sheet and place them under the broiler, watching constantly. Toast the meringue for about 30–60 seconds until browned to your liking, rotating the pan as necessary for even toasting. Remove when toasted. Repeat with the remaining cupcakes.
If desired, drizzle cupcakes with homemade or store-bought hot fudge. Serve.