Preheat the oven to 450 degrees . Arrange the zucchini on a baking sheet, cut side down; coat with cooking spray and season with salt and pepper. Roast until softened and beginning to brown, 8 to 10 minutes.
Meanwhile, salt the eggplant and let it sweat on a kitchen towel for a few minutes. In a medium skillet over medium-high heat, warm the EVOO, three turns of the pan. Add the onion, garlic, roasted red pepper, thyme and crushed red pepper; season. Cook, stirring, for 5 minutes. Add the eggplant, partially cover and cook until very tender, 10 to 12 minutes. Stir in the diced tomatoes.
Remove the zucchini from the oven; fill with the vegetable mixture. Sprinkle with the grated cheese, then top with the sliced mozzarella. Garnish each pizza with a few tomato slices. Return to the oven and bake until the cheese begins to brown, 5 to 8 minutes. Garnish with the basil. Cut into pieces if desired.