Heat oven to 360°F. Prepare two baking sheets with a layer of foil (do not use parchment paper as it may burn when toasting the marshmallows).
Cream the butter, sugar, and honey in the bowl of stand mixer until combined, about 3 minutes. Add vanilla, then the egg, mixing for a minute between each addition.
In a separate bowl, whisk together the dry ingredients (baking soda, salt, flours, and spices). Add the dry mixture to the wet ingredients one-third at a time, mixing between each addition until a dough forms. Remove from the mixer and fold in the chocolate chips.
The dough may be quite wet – if so, chill in the fridge for at least 10 minutes. When ready to bake, roll the dough into balls around one to two tablespoons large. Space them out on the baking sheets, leaving plenty of room around each. If desired, press a milk chocolate square flat into the top of each ball of dough.
Bake for 11-12 minutes, then remove the baking sheets from the oven and let the cookies rest for at least 5 minutes. Top each cookie with a halved large marshmallow (or a few mini marshmallows) and brulee gently with an oven torch. Be mindful, as the sugars of the marshmallows can light on fire quickly!
Alternatively, you can toast the marshmallows under your broiler. Top the cookies with the marshmallows as above, and place the baking sheet under the broiler for one to two minutes. Watch carefully as they can burn quickly! I recommend doing a few at a time, as oven temperatures can vary you and you don't want to burn the whole batch at once.
Serve warm, or store in an airtight container at room temperature for three to five days.