Preheat the oven to 375 degrees F (190 degrees C). Lightly spray a 9x13-inch baking dish with cooking spray.
Bring a large pot of lightly salted water to a boil. Add penne and cook, stirring occasionally, until tender yet firm to the bite, about 11 minutes. Drain.
Heat oil in a large Dutch oven over medium heat. Add garlic and fennel seeds; cook and stir for 1 minute. Pour in pasta sauce, 1/4 cup basil, and tomato paste; simmer, stirring frequently, until sauce is heated through, 10 to 15 minutes.
Meanwhile, mix remaining 1/2 cup basil, ricotta, roasted peppers, Parmesan cheese, eggs, and salt together in a medium bowl.
Spread 1 cup tomato sauce in the bottom of the prepared dish. Cover with 1/2 of the penne, 1/2 of the remaining tomato sauce, all of the ricotta mixture, remaining penne, all the meatballs, and remaining sauce. Cover baking dish with foil.
Bake in the preheated oven until meatballs are heated through, about 30 minutes. Uncover casserole and cover with mozzarella cheese. Continue baking until cheese is melted, about 10 minutes more. Let stand for 15 minutes before serving.
