Place beans in a medium bowl. Add enough cold water to cover by 2 inches. Let soak overnight. Drain, and set aside.
In a large pot, combine 8 cups of water, drained beans, and bay leaf. Bring to a boil. Reduce to a simmer, and cook, partially covered, until beans are almost tender, about 1 hour.
In a medium saute pan, heat oil over medium heat. Add onion, garlic, carrot, celery, rosemary, and 2 teaspoons thyme. Cook, covered, until onions begin to soften, about 10 minutes. Stir in tomatoes, and bring to a simmer. Cook for 2 minutes. Add vegetable mixture to beans.
Stir in squash, potato, kale, cheese rind, salt, and pepper. Add enough water to just cover (about 6 cups), and bring to a boil. Reduce to a simmer, and cook, covered, until potatoes and beans are tender, about 25 minutes.
If desired, to thicken the soup, use the back of a spoon to mash about 2 cups of beans, squash, and potato against the side of the pot. Add sage, remaining teaspoon of thyme, and crushed red pepper. Taste, and adjust for seasoning. Garnish with grated cheese and a drizzle of olive oil, if desired. Serve immediately.