Bring a large pot of lightly salted water to a boil. Cook elbow macaroni in the boiling water, stirring occasionally until cooked through but firm to the bite, about 8 minutes. Drain and transfer pasta to the prepared baking dish.
Place eggplant slices in a large pot of lightly salted water. Let eggplant soak to help remove some of the bitterness, about 30 minutes. Drain and pat eggplant strips with a paper towel to dry; transfer to a baking sheet. Brush eggplant with about 2 tablespoons olive oil; season with 2 teaspoons garlic powder, salt, and pepper.
Heat a large skillet over medium-high heat; saute eggplant until slightly browned, 5 to 10 minutes. Spread cooked eggplant over pasta.
Pour 2 tablespoons olive oil into the same skillet; saute onion and mushrooms until tender, 5 to 10 minutes. Spread onion mixture over eggplant layer.
Season chicken thighs with garlic powder, salt, and pepper to taste.
Pour remaining 2 tablespoons olive oil into the same skillet; cook chicken until browned, about 5 minutes per side. Arrange chicken on the onion layer.
Preheat oven to 400 degrees F (200 degrees C).
Pour wine into the skillet, and bring to a boil while scraping the browned bits of food off of the bottom of the pan with a wooden spoon. Add water, tomato paste, oregano, basil, and rosemary leaves; cook and stir until sauce is smooth and thickened, about 5 minutes. Add chicken to the sauce, cover skillet, decrease heat to low, and simmer while oven preheats, 5 to 10 minutes.
Arrange chicken atop the onion layer and pour sauce over chicken and vegetables. Cover dish with aluminum foil.
Bake in the preheated oven until chicken is no longer pink and the juices run clear, 20 to 30 minutes. An instant-read thermometer inserted in the thickest part of chicken should read 165 degrees F (74 degrees C). Sprinkle Parmesan-Romano cheese over chicken.