Preheat your oven to 425 degrees. Place liners in your muffin tin and spritz them with nonstick spray (don't skip this step!).
Whisk together the flour, baking powder, baking soda, salt, and pumpkin pie spice.
In a separate bowl, combine the squash, agave, extracts, and milk. Add dry to wet in two batches, mixing until almost just combined. Add the chocolate chips or pecans and stir until just incorporated. The batter will be very thick.
Divide the batter between the 12 muffin liners. They will be very fill. Using a spoon spritzed with nonstick spray, smooth the tops out. Sprinkle lightly with the coconut sugar.
Bake for 5 minutes, then adjust the heat down to 375 F (no need to remove muffins from the oven while the temperature changes!). Bake for an additional 10 minutes, adjust the heat to 350 F, and bake an additional 5 minutes.
Store at room temperature for up to three days, freeze for longer storage.
Notes
Nutritional estimate includes chocolate chips. With pecans, calories remain the same but fat increases to 6 g and carbs decrease to 41 g.