Heat a soup pot over medium heat; add the butter and melt. When the butter foams, add the onions, leeks, shallots, garlic, bay leaf, thyme and salt and pepper. Partially cover and cook, stirring occasionally, until caramelized, about 35 minutes. Deglaze the pot with sherry, then add the Worcestershire and stock. Taste for seasoning when it comes to a bubble. Cool and store for a make-ahead meal.
Heat the soup and creme fraiche over medium heat until bubbly and thickened a bit. Toast the bread on the middle rack under the broiler; remove and top one side with the mustard and cheese. Return to the oven to melt the cheese.
Serve the soup in shallow bowls, topped with scallions and cheesy croutons.