2 TBSP unsweetened unsulfured coconut flakes (optional; available at specialty and health food stores), toasted
Preheat oven to 425° F. Cut butternut squash in half vertically then scoop out seeds with a spoon and discard. Season the cut sides of the butternut squash halves with a pinch of salt and ground black pepper.
Place butternut squash cut sides down on a baking sheet lined with parchment paper. Place in oven and bake for 15 minutes.
After squash has been in oven for 15 minutes, add apples, cut side down, to baking sheet in oven and cook squash and apples an additional 30 minutes, until both are tender when pierced with fork.
Remove squash and apple from oven and set aside for a few minutes until cool enough to handle.
In a large soup pot, sauté shallot and garlic in olive oil, stirring frequently over low heat until softened and caramelizing, about 7-8 minutes
Remove shallot pan from heat. Scoop flesh of squash out from skins and add squash, apples, and 4 cups broth to shallot pan. Using immersion blender, process until fully blended and smooth. Alternatively, ingredients can be added to high speed blender in batches and processed until smooth.
Stir in maple syrup, almond milk, nutmeg, and cinnamon and blend again until smooth. Add additional broth if necessary to achieve desired consistency.
Return soup to burner and heat over low flame. Do not allow to boil.
Serve warm, garnished with toasted pepitas and coconut flakes.