To prepare the graham cracker cups, combine the butter, brown sugar, and honey in the bowl of a standing electric mixer fitted with the paddle attachment. Beat until fluffy, about 5 minutes.
Whisk flours, salt, and cinnamon in a small bowl to combine.
Add the dry ingredients to the butter mixture in three additions, beating until just combined after each addition. Beat the mixture for about 1 minute after the final addition to ensure even distribution of ingredients. Wrap the dough tightly in plastic wrap and refrigerate for about 30 minutes before rolling (if you refrigerate it for much longer, let it soften a bit before rolling it out).
Lightly grease 18 cups in two standard-sized muffin tins.
Unwrap the dough and divide in two pieces. Place one piece of dough between two sheets of parchment paper. Roll the dough to a thickness of about 1/8 inch. Peel away the top layer of paper and dust the dough lightly with flour. Replace the paper, flip the dough over, and remove the other piece of parchment paper. Using a 3¾-to 4-inch flower-shaped cookie cutter, stamp out as many flowers as possible. Gently transfer the dough to muffin tins, tucking each flower gently into one of the cups. The dough will be fragile; if you have difficulty transferring the flowers, you may need to dust with more flour before cutting the shapes.
With a toothpick or sharp skewer, prick holes in the dough around the bottom edge of the cup, about 1/8 to 1/4 inch apart, adding a few holes in the center as well. Gather the scraps for re-rolling and hold them until you’ve rolled and stamped flowers from the second piece of dough. Combine remaining dough with the reserved scraps and re-roll.
Transfer muffin tins to the refrigerator for at least 15 minutes before placing them in an oven preheated to 350° F. Bake for 10 to 12 minutes, until just set, shifting the baking sheets halfway through for even baking. Let the cookies cool in the muffin tins for 15 to 20 minutes before removing them carefully with a thin spatula.
While the cups cool, place chocolate in a 2-cup measuring glass with a pour spout. Bring cream to a boil over medium heat. Pour cream over the chocolate and let it sit without stirring for two minutes before mixing vigorously with a small spatula. Once the chocolate becomes smooth and glossy, add vanilla extract and mix until smooth. Working quickly, pour ganache into the prepared graham cracker cups, filling them about ? of the way full. If the ganache begins to look grainy, mix with a spatula to smooth it before continuing.
To finish in the oven, preheat the broiler. Place ganache-filled cups on a baking sheet and top each cup with a handful of mini marshmallows. Place the baking sheet on the top rack of the oven, and, watching carefully, toast the marshmallows to desired doneness. Serve immediately.
To finish around the campfire, toast large marshmallows on the end of long sticks to desired doneness. Carefully scrape marshmallows onto the ganache-filled cups. Eat immediately.