French Onion and Mushroom Pasta Bake

Name: French Onion and Mushroom Pasta Bake
Ingredients: Olive oil; 2 yellow onions, peeled and sliced; Kosher salt; 8 ounces white button mushrooms or cremini mushrooms, sliced; 6 tablespoons of unsalted butter; 1 teaspoon fresh thyme leaves (from about 3 sprigs); 6 tablespoons all-purpose flour; 1 1/2 cups beef broth (or water); 1 1/2 cups milk; 1/2 teaspoon crushed red pepper; 1 teaspoon Dijon mustard; Freshly ground pepper; 1 cup grated Gruyere + 1/2 cup grated Gruyere (for the topping); 1 cup grated mozzarella (about 5 ounces) + 1/2 cup grated mozzarella (for the topping); 1 pound of pasta of choice (I used rigatoni); 2 tablespoons unsalted butter; 2 cups cubed bread