Preheat oven to 425 degrees F (220 degrees C). Grease an 8x14-inch baking dish.
Mix seasoned bread crumbs, 1/4 cup Parmesan cheese, and red pepper flakes in a shallow bowl. Brush eggplant slices with olive oil and press into bread crumb mixture to coat. Lay slices onto a baking sheet and bake in the preheated oven until browned and tender, about 15 minutes. Remove eggplant and reduce oven temperature to 375 degrees F (190 degrees C).
Whisk tomato paste and water in a saucepan, place over medium heat, and bring to a simmer. Stir in basil, oregano, parsley, garlic, brown sugar, sea salt, and black pepper.
Place eggplant slices into prepared baking dish, overlapping the slices. Spoon tomato sauce over eggplant and top with mozzarella cheese and 3/4 cup Parmesan cheese.
Bake in the preheated oven until cheese is melted, about 15 minutes. If desired, broil for 1 to 2 more minutes to give the cheese topping a golden color. Let stand for 5 minutes before serving.