Preheat your oven to 400°F. Cut the butternut squash in half and drizzle it with olive oil to coat. Place the squash halves face down on a baking sheet and transfer to the oven. Roast until the squash is tender, about 25 to 30 minutes. Remove the baking sheet from the oven and let the squash cool enough to handle. Scoop the flesh out and blend or process in a blender or food processor until smooth. Refrigerate the puree in an airtight container until you need it for the muffins. I always make extra puree to keep on hand for soups or other baked goods.
In a large bowl, combine the eggs, maple syrup, melted coconut oil, 1/2 cup of the prepared butternut squash puree (from Step 1), and vanilla extract. Sift the coconut flour, tapioca flour, fine sea salt, grain-free baking powder, ground cinnamon, and grated fresh nutmeg into the wet ingredients. Whisk until the batter is fully incorporated and smooth. For a slightly spicier muffin, I like to add a pinch more cinnamon.
Line a muffin tin with six paper liners. Divide the prepared batter (from Step 2) evenly among the liners. Set the muffin tin aside while you prepare the pecan topping. In a small bowl, mix together maple sugar, maple syrup, chopped pecans, tapioca flour, coconut oil, ground cinnamon, and a pinch of sea salt. Sprinkle this mixture generously over each filled muffin cup.
Bake the muffins in the preheated oven at 400°F for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely. I like to enjoy these muffins warm with a touch of extra maple syrup drizzled on top.