Microwave 3 onions, ¼ cup chili powder, ¼ cup tomato paste, 3 Tablespoons oil, 8 minced garlic, 2 Tablespoons cumin and 1 Tablespoon oregano in large bowl, stirring occasionally, until the onions are softened, about 5 minutes; transfer to slow cooker.
Stir, 30 ounces beans, 28 ounces tomato puree, 2 cups broth, ¼ cup tapioca, 3 Tablespoons soy sauce, 1-2 Tablespoons chipotles, 2 Tablespoons sugar, and 2 bay leaves into slow cooker. Season beef with salt and pepper and nestle into slow cooker. Gently stir together. Cover and cook until beef is tender, 9 to 11 hours on low or 5 to 7 hours on high.
Let chili settle for 5 minutes, then remove fat from surface using large spoon. Discard bay leaves. Season with salt, pepper and sugar to taste, sprinkle with toppings and serve.