Prep. Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone baking mats.
Mix dry ingredients. In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon, and salt. Set aside.
Mix the wet ingredients. In a large mixing bowl, beat the dairy free butter, brown sugar, and white sugar until light and fluffy (about 2–3 minutes).Then, mix in the egg, egg yolk, and vanilla extract until smooth. Combine everything. Slowly add the dry ingredients to the wet, mixing just until combined.
Add the mix-ins. Stir in the chopped chocolate and graham cracker crumbs until evenly distributed. The dough will be thick.
Stuff the cookies. Using a medium cookie scoop, scoop two balls of dough per cookie (about 3 tablespoons total). Flatten one scoop slightly, place half a marshmallow in the center, and top with the second scoop. Gently seal the edges and roll into a ball to fully enclose the marshmallow. Repeat until all cookies are assembled and placed on lined baking sheets.
Chill the dough. Place the baking sheets with the formed cookies into the fridge and chill for at least 30 minutes before baking.
Bake the cookies. Place stuffed dough balls on prepared baking sheets, spacing them 2–3 inches apart. Bake for 10–12 minutes, or until edges are golden and centers look just set.
Garnish and cool. Remove the cookies from the oven and allow cookies cool on the baking sheet for 5 minutes before transferring to a wire rack. If desired, sprinkle with flaky sea salt while still warm.