Preheat the oven to 350 degrees. Line a small baking sheet with aluminum foil. Cut the neck off the squash and set it aside. Cut the bulb in half and scoop it out and discard the seeds.
Brush each half inside and out with about 1½ teaspoons of the olive oil. Sprinkle the cavities with salt and pepper and tuck a sprig of sage into each. Cut side down on the baking sheet and roast until completely tender, about 1 hour.
Remove the squash from the oven and let it cool, then scoop out and reserve the flesh (discard sage).
While bottom half is roasting, using a paring knife, peel away the skin from the neck of the squash until you reach the bright orange flesh. Cut the flesh into ½-inch pieces (you should have about 4 cups).
Put the remaining oliveoil in a stockpot over medium-high heat, add the leeks, carrots, shallots, and onions, and cook, often stirring, for about 6 minutes.
Add the diced squash, garlic, 1½ teaspoons salt, and ½ teaspoon pepper and cook gently for 3 minutes, reducing the heat as necessary to keep the garlic and squash from coloring. Stir in the honey and cook, stirring, for 2 to 3 minutes.
Add the stock and bouquet garni, bring to a simmer and cook for 10 to 15 minutes or until the squash is tender.
Add the roasted squash and simmer gently for about 30 minutes for the flavors to blend. Remove from the heat and discard the bouquet garni. Transfer the soup to a blender in batches, and purée. Strain the soup through a fine sieve into a bowl. Taste the soup and adjust the seasoning.
In a small skillet, add the butter and rotate the skillet over the heat to brown the butter evenly, scraping up any bits that settle in the bottom. As soon as the butter is a hazelnut brown, pour it into the pot of soup -- keep a safe distance, it may sputter -- then stir.
Ladle the soup into six serving bowls. Top each with a dollop of crème fraîche. Grind some black pepper over the top and sprinkle on the chives. Drizzle a little olive oil over the top.