Preheat the oven to 400 degrees F. Line a large cookie sheet with parchment paper. Cut the butternut squash in half lengthwise and scoop out the seeds. Set the butternut halves onto the cookie sheet. Season generously with kosher salt and fresh ground black pepper. Place the cubed unsalted butter into the cavities of the butternut squash. Roast the squash for 45 minutes to 60 minutes, or until fork tender.
Line a smaller cookie sheet with parchment paper. Place the bacon and/or pancetta on the lined cookie sheet. Bake at 400 degrees F until crispy (roughly 11-15 minutes). Transfer the cooked bacon and/or pancetta to a paper towel to drain. Crumble up the bacon and set aside.
Over medium heat warm up a large Dutch oven. Drizzle in the 2 tablespoons of olive oil. Add in the onions and a few sprinkles of kosher salt as well as black pepper. Periodically stir the onions until soften/slightly caramelized, roughly 5-6 minutes. Add in the crushed garlic cloves, granulated sugar, fresh grated nutmeg, the chopped carrot, a sprig of thyme, and 1 cup of the chicken stock. Stir well.
Scoop the squash out of the skins into the large dutch oven. Add in the remaining chicken stock and thyme sprigs. Season to taste. Bring the soup to a rapid boil with stirring frequently. Reduce the heat and allow the soup to simmer for 1 hour.
Remove the Dutch oven from the heat. Using a hand immersion/blender puree the soup until a thick creamy smooth consistency is reached. Reheat the soup if necessary.
Ladle the soup into desired serving bowls. Garnish the soup with the crispy bacon and leaves from a few sprigs of thyme. Enjoy.