Preheat oven to 375 degrees F.
In a large skillet, heat 2 tablespoons oil over medium heat. Add onion and garlic and cook 7 minutes, stirring occasionally, until onion is tender.
Add squash and bell pepper, sprinkle with 1/2 teaspoon salt, and cook 7 to 10 minutes, stirring occasionally, until squash is tender. Stir in basil and 2 tablespoons Parmesan.
Spoon mixture into an 11" x 7" baking dish. Top with tomato slices and sprinkle with remaining 1/4 teaspoon salt. Scatter panko and remaining 1/2 cup Parmesan over the top and drizzle with remaining 1 tablespoon oil.
Bake 20 minutes, or until topping is crisp and vegetables are piping hot. Serve hot or at room temperature.