Preheat oven to 400°.
To prepare the green tomatoes, combine flour and next 4 ingredients (flour through sugar) in a shallow dish. Dip tomato slices in milk; dredge in flour mixture. Lightly coat both sides of tomato slices with cooking spray.
Place a baking sheet in oven; heat at 400° for 5 minutes. Remove from oven; immediately coat with cooking spray. Place tomato slices on preheated baking sheet. Bake at 400° for 25 minutes, turning after 15 minutes.
To prepare the gravy, melt butter in a medium nonstick saucepan over medium heat. Add mushrooms and onion, and cook 4 minutes or until tender, stirring frequently. Add chopped red tomato; bring to a boil, and cook for 10 minutes or until liquid almost evaporates. Stir in 1/4 teaspoon salt and 1/4 teaspoon pepper. Spoon the gravy over the tomato slices.