Melt together the butter, onions, and honey in a large Dutch oven over medium-high heat. Cook, stirring occasionally until softened, about 10 minutes. At this point, you want to slowly add the wine, a little at a time until the wine cooks into the onions. Continue to cook another 10-15 minutes until you've used the wine and the onions are deeply caramelized.
Add the garlic, mushrooms, thyme, and sage. Season with salt and pepper, cook another 3-4 minutes. Add the broth, Worcestershire sauce, bay leaves, and a pinch each of salt and pepper. Increase the heat to medium-high and return the soup to a simmer, simmer 10 minutes. Remove the bay leaves and discard. Season to taste with salt and pepper.
Meanwhile, preheat the oven to 400° degrees F. Arrange the bread on a baking sheet and toast for 10-15 minutes, until very dry. Switch the oven to broil.
Ladle the soup into oven-safe bowls. Add a slice of bread to each, and top evenly with cheese. Place each soup bowl on a baking sheet and transfer to the oven, broil until bubbly and golden brown, 3 to 5 minutes. Top with fresh thyme.