For the soup: Melt the butter in a large Dutch oven or pot over medium heat. Add half of the onions and season with 1/4 teaspoon salt and a few grinds of pepper. Top with the remaining onions and season with 1/4 teaspoon salt and a few more grinds of pepper. Add the bay leaves and thyme. Cook, stirring occasionally, until all of the liquid evaporates the onions are very soft and just begin to turn golden, 45 minutes to 1 hour.
Add the white wine, bring to a simmer and cook, stirring, until almost completely evaporated, about 6 minutes. Pour in the beef broth and 1 cup water, bring to a high simmer and cook until the soup has reduced to 5 cups, 30 to 40 minutes. Season with salt and a few grinds of pepper. Remove the bay leaves and thyme. Either keep warm on a low burner or cool completely, refrigerate and reheat later. (The soup can be made and refrigerated up to 2 days in advance or frozen for up to 1 month).
For the mac 'n' cheese: Bring a medium pot of water to a boil, add the macaroni and cook according to package instructions. Drain, reserving 1/2 cup of the cooking liquid.
Melt the butter in a medium saucepan over medium heat. Whisk in the flour until smooth, about 2 minutes. Gradually whisk in the milk and reserved pasta water and stir until thick, about 4 minutes. Stir in 1 cup each of the cheeses, 1/2 teaspoon salt and a few grinds of pepper; stir until melted and smooth. Remove from the heat and stir in the cooked pasta until coated. Let cool slightly, stirring frequently.
Preheat the oven to broil. Place the soup crocks on a rimmed baking sheet and divide the hot soup among the crocks or bowls, filling about three-quarters of the way. Top each with a quarter of the mac 'n' cheese (some will sink into the soup, which is fine). Evenly sprinkle with the remaining cheeses and the panko. Grill until the cheese is melted and golden brown in spots, 2 to 3 minutes (the soup will bubble and some may spill out). Serve hot.
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