For the topping:
1/4 cup fresh breadcrumbs
1/3 cup grated Parmesan cheese
1 tablespoon olive oil
2 teaspoons finely chopped fresh parsley leaves
2 teaspoons finely chopped fresh thyme leaves
For the gratin:
2 medium zucchini squash (about 1 1/2 inches in diameter)
2 medium yellow zucchini (about 1 1/2 inches in diameter)
3 to 4 plum or Roma tomatoes
1/4 cup olive oil, divided
1 1/4 teaspoons kosher salt, divided
1/4 teaspoon freshly ground black pepper
1 small onion, thinly sliced
1/2 medium orange bell pepper, halved and thinly sliced
3 cloves garlic, minced
Arrange a rack in the middle of the oven and heat to 375°F. Lightly coat an 8x8-inch baking dish with oil; set aside.
Make the topping:
Place all the ingredients in a small bowl and mix until combined; set aside.
Make the gratin:
Use a mandoline or a very sharp knife to cut the zucchini, yellow squash, and tomatoes crosswise into 1/4-inch rounds. Place in a large bowl, add 2 tablespoons of the oil, 1 teaspoon of the salt, and the pepper. Toss to combine; set aside.
Heat the remaining 2 tablespoons oil in a large frying pan over medium heat until shimmering. Add the onions, bell pepper, and remaining 1/4 teaspoon of salt. Cook, stirring occasionally, until the onions are tender and lightly browned, 10 to 12 minutes. Stir in the garlic and cook until fragrant, about 1 minute more.
Transfer the onion mixture to the baking dish and spread into an even layer. Place the zucchini, squash, and tomato slices on the onions, arranging them on their sides and alternating the slices as you go. Sprinkle the breadcrumb mixture over the top. Cover tightly with aluminum foil.
Bake for 30 minutes. Uncover and bake until the vegetables are tender and the edges and topping are browned, 15 to 20 minutes more.