Heat a large nonstick skillet over medium heat. Add 4 teaspoons oil; swirl to coat. Add onion; cook 3 minutes. Add bell pepper; cook 2 minutes. Add squash and garlic; cook 4 minutes. Place vegetable mixture in a large bowl. Stir in quinoa, 1/4 cup basil, thyme, 1/2 teaspoon salt, and black pepper.
Combine remaining 1/4 teaspoon salt, milk, cheese, and eggs in a medium bowl, stirring with a whisk. Add milk mixture to vegetable mixture, stirring until just combined. Spoon mixture into an 11 x 7inch glass or ceramic baking dish coated with cooking spray.
Place bread in a food processor; pulse until coarse crumbs form. Return skillet to medium-high heat. Add remaining 1 teaspoon oil to pan; swirl to coat. Add breadcrumbs; cook 3 minutes or until toasted. Arrange tomatoes evenly over vegetable mixture. Top evenly with breadcrumbs. Bake at 375° for 40 minutes or until topping is browned. Sprinkle with remaining 1/4 cup basil.