Melt the butter with the olive oil in a large Dutch oven over medium heat. Add the onions and salt. Cook for 10 minutes, stirring often, until the onions soften. Reduce the heat to medium-low and continue cooking for 45 to 55 minutes, stirring every few minutes, until the onions are deeply golden brown and silky. If the pot becomes dry, add 1 tablespoon water and scrape up the browned layer.

Stir in the garlic and cook for 30 seconds. Sprinkle in the flour and cook for 1 minute, stirring continuously, so it loses its raw taste.

Pour in the white wine and scrape the bottom of the pot. Simmer for 3 to 5 minutes, until the wine has reduced by about half.

Add the beef stock, thyme, bay leaf, and black pepper. Bring to a gentle simmer and cook uncovered for 30 minutes. Remove the thyme stems and bay leaf, then taste and adjust the salt and pepper.

While the soup simmers, heat the oven to 400°F (200°C). Arrange the baguette slices on a rimmed baking sheet and toast for 8 to 10 minutes, turning halfway, until dry and golden on both sides.

Preheat the broiler. Set 6 broiler-safe bowls on the baking sheet and divide the hot soup among them. Top each bowl with 2 toasted baguette slices, Gruyère, and optional Parmesan. Broil for 2 to 4 minutes, watching closely, until the cheese is melted, bubbling, and browned in spots. Serve carefully; the bowls will be very hot.