Cook the pasta according to the package directions.
Meanwhile, whisk together the vinegar, 1/2 teaspoon of the salt, and 1 tablespoon of the oil in a small bowl. Place the zucchini, eggplants, and onion on a baking sheet. Brush with the vinaigrette. Heat broiler on high. Broil until tender, 8 minutes per side.
Heat oven to 350° F. Chop the roasted vegetables. Place a large pot over low heat. Add the garlic and the remaining oil and cook for 3 minutes. Add the drained pasta, vegetables, oregano, tomatoes, pasta sauce, Feta, black pepper, red pepper flakes, and the remaining salt and toss. Transfer to a 9-by-13-inch baking dish. Sprinkle with the mozzarella. Cover and bake for 30 minutes. Uncover and bake for 20 minutes more.
To Freeze: Assemble (but do not bake) the casserole. Cover tightly with two layers of aluminum foil. Store for up to 3 months.
To Reheat: Thaw overnight in the refrigerator or thaw partially in the microwave. Cover and heat in a 350° F oven for 30 minutes. Uncover and heat for 10 minutes more.
Tip: To make individual servings, freeze the pasta in ramekins or small ovenproof bowls. Cover and heat for 20 minutes, then uncover and heat for 10 minutes more.