For the stock: Roughly chop the celery, carrots (skin on), onion (skin off), and fennel (including fronds) into large chunks and place in a large stock pot. Add the garlic, butternut squash, and water. Make a bouquet garni by wrapping the cloves, cinnamon, allspice, and thyme in cheesecloth. Add it to the stock pot and bring to a boil; then reduce to a simmer and cook uncovered for 1½ hours. Strain and set aside to cool slightly while finishing the soup. Note: Stock can be made in advance and stored in the refrigerator up to one week, freezer up to one month.
Roast the vegetables: Preheat oven to 400 F. In a roasting pan, add squash, shallot, and garlic. Season with salt and combine. Then add thyme, bay leaves, chili, 1/4 cup of oil, and vinegar. Lightly toss and roast in the oven until tender and cooked through, about 35 minutes.
Assemble the soup: Make a finishing sauce by combining 1 cup kefir with ¼ cup oil, lemon zest, salt, and pepper. Set aside. When the vegetables are roasted, remove the aromatics (thyme, bay leaves, chili) and blend with 6 cups of the vegetable stock. With the blender on low speed, add 1/4 cup oil and 1 cup kefir. Remove the blender top, taste, and add salt as needed, blending to combine. Serve the soup with kefir sauce drizzled on top.