Prepare Baking Station: Position oven racks in the upper and lower thirds and preheat the oven to 375°F (190°C). Line your baking sheets with parchment paper.
Whisk Dry Staples: In a medium mixing bowl, thoroughly whisk together the white whole-wheat flour, low-sodium baking powder, cinnamon, and nutmeg.
Cream Butter and Sugars: In the bowl of a stand mixer, beat the softened butter with the brown and coconut sugars on medium-high speed for 1-2 minutes, until combined (it may not get light and fluffy).
Incorporate Eggs and Wet Ingredients: Reduce mixer speed to low. Add the eggs one at a time, followed by the applesauce and vanilla, mixing until just combined.
Combine Wet and Dry: With the mixer on its lowest setting, gradually add the flour mixture until just combined. Do not overmix.
Fold in Final Ingredients: Remove the bowl from the mixer. Using a spatula, gently fold in the rolled oats and dark chocolate chunks.
Portion the Dough: Using a small (1-tablespoon) cookie scoop, drop rounded portions of dough about 2 inches apart onto the prepared baking sheets.
Bake to Perfection: Bake for 8 to 10 minutes, rotating the sheets halfway through, until the edges are firm and lightly golden-brown. Cool on the pan for 3 minutes before transferring to a wire rack.