Preheat oven to 425°F. Line two large, rimmed baking sheets with parchment paper. On one baking sheet, toss the eggplant with 2 Tbsp olive oil. Arrange in a single layer and set aside. On the other baking sheet, toss the bell pepper, zucchini and yellow squash with 1 Tbsp olive oil, arrange vegetables in a single layer. Sprinkle both pans with salt to taste. Place pans in oven and bake 20 minutes. Meanwhile, warm 1 Tbsp olive oil in a soup pot. Add onion and 1/8 tsp salt. Cook, stirring occasionally, until the onion is tender and caramelizing on the edges, about 8 to 10 minutes. Add garlic and cook until fragrant, about 30 seconds.
Add tomatoes and simmer. Transfer all veggies into tomato sauce. Stir in fresh basil, red pepper flakes, oregano, pepper, and more salt, if needed. Simmer 5-10 minutes, until tomatoes release their juices to create the sauce for the dish. Serve with thick slices of warmed crusty bread or baguette.