Preheat oven to 350°. Spray a 13x9-inch baking dish with cooking spray.
In a Dutch oven, heat 2 tablespoons oil over medium-high heat. Add 1 cup onion and 3 minced garlic cloves; cook, stirring frequently, for 5 minutes or until onion begins to soften. Stir in crushed tomato, next 4 ingredients, and ½ teaspoon salt, and bring to a boil. Reduce heat, and simmer, stirring occasionally, for 25 minutes.
In a large skillet, heat remaining 1 tablespoon oil over medium-high heat. Add squash, remaining 1½ cups onion, and remaining minced garlic clove; cook, stirring occasionally, for 5 minutes or until vegetables begin to soften. Sprinkle with flour and remaining ½ teaspoon salt; cook, stirring constantly, for 2 minutes. Stir in sour cream, 1 cup cheese, and 1 tablespoon cilantro until melted and smooth.
Spread ½ cup cooked tomato mixture in bottom of prepared pan. Spoon about ¼ cup squash mixture in center of each tortilla, roll up, and place seam side down in pan. Pour remaining sauce onto rolled tortillas, and sprinkle with remaining 1 cup cheese.
Bake for 25 to 30 minutes or until golden brown and bubbly. Garnish with tomato and green onion, if desired.
Recipe by Paula Deen Magazine at https://pauladeenmagazine.com/cheesy-squash-enchiladas-recipe/