Baked Pasta with Tomatoes and Eggplant

Name: Baked Pasta with Tomatoes and Eggplant
Ingredients: Kosher salt and freshly ground black pepper; 8 ounces penne rigate and/or fusilli; 3 cups Tomato and Eggplant Soup, recipe follows; 4 ounces fresh mozzarella, medium-diced; 5 tablespoons freshly grated Italian Parmesan cheese, divided; 2 tablespoons unsalted butter, small-diced; Good olive oil; 4 1/2 cups (1/2-inch-diced) unpeeled eggplant (1 pound); 2 cups chopped yellow onion (2 onions); 2 cups chopped fennel bulb; 2 tablespoons minced garlic (6 cloves); 3 cups good chicken stock, preferably homemade; 1 (28-ounce) can crushed tomatoes, preferably San Marzano; 2 teaspoons whole dried fennel seeds; 1 1/2 teaspoons dried oregano; 1 teaspoon fresh thyme leaves; 1/4 teaspoon crushed red pepper flakes; 1 (28-ounce) can whole peeled tomatoes, preferably San Marzano; Freshly grated Italian Parmesan cheese, for serving