Set an oven rack in highest position and preheat oven to 350°. Heat 2 tbsp. oil in a 4-qt. saucepan over medium heat. Add onion and garlic; cook until translucent, about 4 minutes. Add wine and let reduce by half, 5 minutes. Stir in tomatoes, salt, sugar, pepper, and chile flakes and simmer, stirring often, until very thick, 20 minutes.
Lay eggplant slices meanwhile on a greased broiler pan (they can overlap). Cover with foil. Bake until steamy and softened, 20 minutes. Uncover; brush with 1 tbsp. oil. Broil until starting to brown, then turn over and brush with remaining oil. Broil until lightly browned, 8 minutes total.
Put an eggplant slice on an oven-safe plate (leave broiler on). Top with 1/4 cup tomato sauce. Lay another slice of eggplant across first and spoon more sauce on top. Top with 2 slices cheese. Repeat layering on 3 more plates.
Broil 2 plates at a time just to melt cheese, about 2 minutes. Sprinkle each plate with about 2 tbsp. each mixed herbs and croutons. Serve with remaining sauce.
Note: Nutritional analysis is per serving.