Set a 12-inch electric skillet to 250ºF, or set a 4-quart saucepan over low heat.
Peel the onions. Halve the onions end to end, then slice into thin half-moons.
Melt the butter in the skillet. Add the onions to the skillet in 3 layers, adding about 1 teaspoon of salt to the top of each addition. Let the onions sweat for 15 to 20 minutes without stirring; do not let the onions sizzle or brown. Continue to cook, stirring occasionally, until the onions are dark mahogany and reduced to approximately 2 cups, 45 minutes to 1 hour.
Add just enough wine to cover the onions (you might not use all the wine, and that's OK), then turn the heat to 375ºF (or high). Cook until the wine is reduced to a syrup consistency, 5 to 10 minutes. Add the beef consommé, chicken broth, and the bouquet garni. Reduce the heat and simmer for 15 to 20 more minutes.
Meanwhile, set an oven rack in the top third of the oven and set the broiler to high. Cut the bread into rounds that will fit into the tops of the crocks. (You can do this with the crocks by inverting them over the bread and pressing down, like a cookie cutter.) Place the bread slices on a half-sheet pan and broil until they just start to brown, about 1 minute.
Season the soup with pepper and Cognac, if using. Place 8 oven-safe crocks on a half-sheet pan and ladle in the soup, leaving about 1 inch of space at the top. Place the toast rounds, toasted side down, on top of the soup and top with the cheese. Broil until the cheese is bubbly and golden, 1 to 2 minutes.