Prep the oven and eggplant: Preheat your oven to 425°F (220°C). Line a baking sheet with parchment paper or foil. Arrange eggplant slices in a single layer, brush both sides with about 2 tablespoons olive oil, and sprinkle with ½ teaspoon salt and some black pepper.
Roast the eggplant: Bake for 20-25 minutes, flipping halfway through, until golden and tender. Remove from oven and reduce temperature to 375°F (190°C).
Cook the sausage mixture: While the eggplant roasts, heat the remaining tablespoon of oil in a large skillet over medium heat. Add the sausage, breaking it into crumbles as it cooks (about 5-7 minutes). Add the diced onion and bell pepper, cooking until softened (about 5 minutes more). Add the garlic, oregano, and red pepper flakes if using, and cook for another minute until fragrant.
Make the sauce: Stir in the crushed tomatoes and tomato paste. Bring to a simmer and cook for 10 minutes, stirring occasionally. Remove from heat and stir in the chopped basil. Season with remaining ½ teaspoon salt and black pepper to taste.
Layer the bake: Lightly grease a 9x13 baking dish. Spread a thin layer of the sauce mixture on the bottom. Arrange half of the roasted eggplant slices over the sauce. Top with half the remaining sauce and half the mozzarella. Repeat layers with remaining eggplant, sauce, and mozzarella. Sprinkle Pecorino Romano on top.
Bake until bubbly: Bake uncovered at 375°F for 25-30 minutes, until the cheese is melted and golden and the edges are bubbling.
Rest and serve: Allow to rest for 10 minutes before serving (this helps it set up for easier cutting). Garnish with additional fresh basil and serve hot.