Preheat oven to 325°. Line 2 baking sheets with parchment. In a large bowl, whisk butter, muscovado sugar, powdered sugar, sour cream, orange zest, if using, and nutmeg until smooth. Fold in whole wheat flour, oat flour, baking powder, baking soda, and salt until a smooth, cohesive dough forms.
Place dough between 2 sheets of parchment and roll to 1/8" thick. Using a 2 3/4" round cookie cutter, cut out rounds (you should get about 16) and arrange on prepared sheets, spacing 1" apart. Using a fork, dock rounds all over.
Bake cookies until edges are golden, 13 to 15 minutes.
As soon as cookies are taken out of the oven, place 15 chips on top of each cookie. Wait until chocolate is melty, about 3 minutes, then evenly spread across cookie with an offset spatula. Let chocolate partially set, about 3 minutes more. Using the tip of offset spatula, draw ridges across chocolate in a back-and-forth motion.
Let chocolate set until hardened before serving.