Prep the zucchini: Slice off the tops and scoop out the insides, leaving about a ¼-inch shell. Lightly salt the inside, then place them cut-side down on a paper towel for about 10 minutes to remove excess moisture.
Cook the filling: In a skillet, heat 1 tablespoon olive oil over medium heat. Add onion and sauté for 3 minutes until softened. Stir in garlic and cook for 30 seconds. Add sausage, breaking it apart, and cook until browned. Add chopped zucchini flesh, diced tomato, chili flakes, salt, and pepper. Cook until most liquid evaporates and mixture looks thick and saucy.
Add the cheese: Turn off heat. Stir in basil, ½ cup mozzarella, and all the Parmesan until melted and creamy.
Stuff the zucchini: Arrange shells upright in a baking dish, drizzle lightly with olive oil, and spoon the filling inside, packing gently. Top each with remaining mozzarella. Place zucchini tops on a small tray.
Bake: Bake at 400°F (200°C) for 20–25 minutes, until the zucchini are tender and the tops golden.
Broil for extra color: Broil for 1–2 minutes to brown the tops.
Serve: Let rest for 5 minutes. Garnish with fresh basil and serve with the roasted lids on the side.