To the slow cooker pot, add the butter, onions, shallots, and honey and stir to combine. Cook on low until the onions are caramelized, stirring once or twice, 4-6 hours.
Add thyme, sage, and flour and cook until lightly browned, about 2 minutes. Stir in wine, broth, Worcestershire sauce, and bay leaves, and season with salt and pepper. Cover and cook 4 to 5 hours more on low, or 2 to 3 hours more on high. Remove and discard the bay leaves. Taste and add more salt and pepper as needed.
Preheat the broiler.
Divide the soup among 6 oven-safe bowls. Add a slice of bread to each and top evenly with cheese. Place the bowls on a baking sheet and broil until the cheese is bubbly and olden brown, 3 to 5 minutes. Top with thyme leaves.