2 pounds ripe red tomatoes (6 medium or 4 large)
1 medium eggplant (1 pound), diced into ½-inch cubes
1 large red, orange, or yellow bell pepper (about 8 ounces), cut into ¾-inch squares
1 medium-to-large zucchini (about 8 ounces), diced into ½-inch cubes
1 large yellow squash (about 8 ounces), diced into ½-inch cubes
5 tablespoons + 1 teaspoon extra-virgin olive oil, divided
¾ teaspoon fine sea salt, divided, more to taste
1 medium yellow onion, chopped
4 cloves garlic, pressed or minced
¼ cup chopped fresh basil
¼ teaspoon red pepper flakes, more or less to taste
¼ teaspoon dried oregano
Freshly ground black pepper, to taste