In a large saucepan, melt 6 tablespoons of the butter over medium heat. Add the shallot, carrot, and celery, and cook until softened, about 5 minutes. Sift the flour over the vegetables, and cook the mixture, stirring constantly with a wooden spoon until it lightens in color, about 2 minutes. Slowly whisk in the milk and bring to a boil. Add the parsley, thyme, and bay leaf. Reduce the heat to low, and simmer, whisking occasionally, until the sauce is thickened, about 30 minutes. Strain and season with 1/2 teaspoon of the salt, nutmeg, and pepper to taste. Place plastic wrap on the surface of the sauce and set aside until ready to assemble the lasagna. (The sauce can be made a day ahead and refrigerated. Reheat before assembling the lasagna. )
Meanwhile, cook the noodles. Bring a large pot of water to a boil, season generously with salt, and boil the lasagna noodles according to package instructions. Drain. Spread the noodles out and layer between pieces of plastic wrap. Set aside.
Preheat the oven to 350 degrees F. Butter an ovenproof 9 x 13-inch casserole dish.
Cover the bottom of the pan with a layer of noodles. Cover with 1 1/2 cups of the meat sauce, 1 cup of the white sauce and 3 tablespoons of the cheese. Repeat to make 3 more layers ending with the remaining meat sauce, white sauce, and cheese. Dot the top with the remaining tablespoon of butter. Bake until bubbly and hot, about 45 to 50 minutes. Remove from the oven and set aside for 10 minutes to firm up before serving.
In a large soup pot or Dutch oven, heat the olive oil over medium heat. Add the pepper flakes and cook for 15 seconds. Add the onion and cook, stirring occasionally, until golden brown, about 15 minutes. Add the garlic and cook until fragrant, about 1 minute. Stir in the tomato paste and cook, stirring constantly, for 1 minute. Add the tomatoes one at a time, crushing them by hand as you go. Season with 1 teaspoon salt and pepper to taste. Simmer the sauce over low heat, covered.
Meanwhile, heat a large skillet over medium-high heat. Add the beef, pork, veal, savory, thyme, oregano, and fennel seeds. Season with 1 teaspoon salt and pepper. Break up the meat with a wooden spoon, and cook until it loses its raw color, about 7 minutes. Add the meat to the sauce, holding back any excess fat. Add the rind of the Parmesan, if using. Simmer the sauce, covered, over low heat, for 1 1/2 hours. (If the sauce gets too thick, adjust the consistency with water.) Season with salt and pepper to taste. Just before serving, remove the Parmesan rind and add the grated cheese.
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