Preheat the oven to 350°F. Line two baking sheets with parchment paper.

In a medium bowl, whisk together the graham cracker crumbs, flour, Dutch-process cocoa powder, baking powder, baking soda, and kosher salt.

In the bowl of a stand mixer fitted with the paddle attachment, or using a hand mixer, beat the softened butter and dark brown sugar together until light and fluffy, about 2–3 minutes.

Scrape down the bowl and add the eggs one at a time, mixing well after each addition. Add the vanilla extract and heavy cream and mix just until incorporated.

Add the dry ingredients to the wet ingredients. Mix on low speed just until the batter comes together and no dry streaks remain. Do not overmix.

Let the batter rest at room temperature for about 20 minutes. This allows the batter to firm up slightly, which helps the cakes hold their shape better while baking.

Using a medium cookie scoop, scoop the batter onto the prepared baking sheets, leaving at least 2 inches between each portion. Gently smooth the tops if needed.

Bake for 10–12 minutes, or until the cakes are set and spring back lightly when gently pressed in the center. Do not overbake.

Allow the cakes to cool on the baking sheet for 5 minutes, then transfer them to a wire rack to cool completely.

Place the chopped dark chocolate in a heatproof bowl.

Heat the heavy cream in a small saucepan over medium heat until steaming and just beginning to simmer. Do not let it boil vigorously.

Pour the hot cream over the chocolate and let sit undisturbed for 5 minutes.

Stir until the chocolate is completely melted and the ganache is smooth.

Set aside at room temperature to cool and thicken to a soft, spreadable consistency. If it becomes too firm, let it sit at room temperature for a few minutes and stir before using.

Add the powdered sugar, vanilla, and pinch of salt. Beat until smooth.

Add the marshmallow creme and beat on medium speed for 2–3 minutes, until fluffy and well combined.

If the buttercream feels too soft to pipe or spread, refrigerate it for 10–15 minutes before assembling.

Pair the cooled chocolate graham cakes by size.

Transfer the marshmallow buttercream to a piping bag fitted with a round tip, or use a spoon or small offset spatula.

Pipe or spread a generous layer of marshmallow buttercream onto the flat side of half of the cakes.

Spread a layer of thickened chocolate ganache onto the flat side of the remaining cakes.

Sprinkle the ganache with a small amount of flaky sea salt, if desired.

Optional: Lightly torch the exposed marshmallow buttercream with a kitchen torch until lightly golden and toasted. Keep the torch moving continuously and use caution (especially with the parchment paper that can catch fire easily).

Gently press one marshmallow-covered cake together with one ganache-covered cake to create a sandwich.

Serve immediately or allow the assembled whoopie pies to sit for several minutes so the filling can set slightly.