In a large, oven-safe skillet, heat the oil over medium-high heat. Add the onions, bell pepper and garlic; cook and stir until tender (4 to 5 minutes). Add the crushed tomatoes and basil the the veggies. Bring to a boil; reduce the heat. Simmer until slightly thickened, about 10 minutes. Remove the skillet from heat.
Layer the sliced veggies into stacks (zucchini, yellow squash, eggplant and tomato). You're going to be arranging the veggie stacks into concentric circles. Transfer the stacks of veggies into the skillet over the tomato mixture, placing them on their sides around the outside edge of the skillet in a circular pattern. Continue adding stacks (making an outside circle, and then inside circles) until the skillet is full.
In a small bowl, combine the topping ingredients, and then brush the mixture over the veggies in the pan.
Cover the veggies with a round piece of parchment paper, and bake until the veggies are almost tender, about 40 minutes. Remove the parchment paper and continue to bake until the veggies are tender and the sauce is bubbling (15 to 20 minutes longer). Let stand for at least 10 minutes before serving.