Step 1: Preheat oven to 375°F. Heat large oven-safe skillet on medium. Add sausage and cook, breaking up into small pieces until browned, 6 to 8 minutes. Remove the sausage to a plate and set aside.
Step 2: Add oil to skillet, then onion and red pepper, and thyme. Season with 1/2 teaspoon salt and pinch of red pepper flakes. Cook, stirring occasionally, until tender, 5 to 7 minutes.
Step 3: Add tomatoes (and their juices) and 2 cups water, then stir in pasta. Bring to a boil, then reduce heat and simmer, covered, 10 minutes (pasta should still have just a slight bite or tightness).
Step 4: Remove from heat and fold in sausage and 1/3 cup each Cheddar and Gruyere. Top with remaining cheese and bake until bubbly, 10 to 12 minutes. Serve sprinkled with Parmesan and parsley if desired.
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