Remove from oven and using a spatula, flip the squash halves over and allow to cool for a few minutes. Using a spoon, scoop all the roasted squash flesh out into a blender or large bowl, being careful not to take any of the skin. Discard squash skins. Set aside garlic confit, which is now ready to use.
In a large soup pot or Dutch oven, add olive oil over medium heat. Add diced onion and 1/2 teaspoon salt. Cook until onion has softened and is translucent, but not browned (melty onions).
When cooked, add onions, 2 cloves of garlic confit and apple to the blender. Add vegetable stock and blend on high-speed for 60 seconds, or until perfectly smooth. Alternatively, if using an immersion blender, add squash, apple, garlic and stock to the onions and blend.
Return the soup from blender to the pot. Add 1/4 - 1/3 cup of maple syrup, to your liking. Grate 1/2 a nutmeg directly into the soup. Add salt and pepper to taste. Stir and bring to a light boil.