Divide the squash/pumpkin (cut-side up), garlic and onions between 2 sheet pans. (Keep the onions and garlic together.) Drizzle over the olive oil and rub to fully coat everything in the oil. Season with the sage, rosemary, thyme and some salt and pepper. Flip the squash so they are cut-side down and roast until fork-tender, 40 to 45 minutes. Allow the squash to cool slightly, about 5 minutes.
While the squash cool, heat the stock and heavy cream in a large pot over medium heat. Add the roasted onions and garlic and bring to a simmer.
Scrape out the flesh of the squash and add to the pot. Using an immersion blender, puree the soup to your desired consistency. Grate over the nutmeg to taste and adjust other seasonings, as needed.
To serve, ladle the soup into bowls and sprinkle over the granola.