Whisk together whole-wheat pastry flour, oat flour, milk powder, baking powder, salt, cinnamon, and nutmeg.
In the bowl of a stand mixer fitted with the paddle attachment, cream butter, sugar, and honey at medium-high speed until light and fluffy, about 2 minutes; scraping down sides of the bowl as needed. Add egg and vanilla and beat at medium to combine. Add half of the flour mixture to mixer and beat at low until nearly combined, add remaining flour mixture and beat until completely combined.
Transfer dough to a sheet of plastic wrap, form into a disk, and wrap tightly; chill in refrigerator for at least two hours for overnight.
When ready to bake, remove dough from refrigerator and let rest at room temperature for 5 minutes. Heat oven to 350°F. Line baking sheets with parchment paper.
On a lightly floured work surface, roll dough to ¼-inch thick.
Stamp out dough with cookie cutters. Transfer cookies to prepared baking sheets spacing ½-inch apart. Bake cookies, one sheet at a time, until cookies are golden and crisp around the edges, 10–12 minutes, rotating sheet halfway through baking. Let cookies cool on sheet 5 minutes then transfer to wire racks to cool completely. Reroll remaining dough and repeat until all is used.