See Notes for easy peeling for the cipollinis and pearl onions.
Preheat the oven to 350 degrees F.
For the “Onion Confit”. Place the sliced onion varieties and garlic into a small baking pan. A loaf pan would work, also. Add enough oil to just cover the veggies. Season with salt and pepper. Stir.
Bake in the oven for 30 minutes. Stir, and continue to bake for another 30 to 45 minutes, or until the confit is bubbling and has some browning.
Remove from the oven and cool for about 30 minutes. Strain through a fine-mesh sieve, reserving all the oil.
Make the soup. In a medium pot or Dutch oven, heat the butter and 2 tablespoons of the reserved oil. Once hot, add the strained onion mixture and stir.
Sprinkle the flour over the onions and stir. Cook the flour for about 2 to 3 minutes, stirring often.
Add the beef stock, Worcestershire, balsamic, thyme, salt and pepper to taste (depending on your stock), and stir. Bring up to a gentle simmer and allow the mixture to thicken slightly. You did not add much flour, so it will not thicken much. You don’t want a thick French Onion Soup; it should still be quite fluid. Simmer for 20 to 30 minutes.
Remove the herbs and taste. Adjust any salt, pepper, balsamic, and/or Worcestershire.
Preheat the broiler to high. Set a rack about 6 to 8” below the broiler (See Notes about pre-toasting the baguette slices.)
Place 4 to 6 individual oven-safe bowls on a baking sheet. Fill the bowls about 1” from the top with the soup. Top each bowl with a baguette slice. Sprinkle the cheese over the bread slices.
Place the baking sheet under the broiler. Do not walk away. Keep an eye on the tops. Remove from the oven once the cheese has melted and is slightly browned, or until your desired browning.
Serve very warm.