Make the Bolognese meat sauce: Heat olive oil in a large stockpot over medium heat. Add the onion and garlic and sauté until softened and fragrant. Add the ground beef and cook until browned, breaking it up as it cooks. Season with salt and pepper to taste.
Deglaze and simmer the sauce: Pour in the red wine and let it simmer until it has evaporated. Add the tomato sauce, cherry tomatoes, and water, then stir in the fresh basil leaves. Cover and simmer over low heat for 2 hours, stirring occasionally.
Prepare the béchamel sauce: Melt the butter in a medium saucepan over medium heat. Add the flour and whisk continuously for about 1 minute. Gradually pour in the milk, whisking constantly to prevent lumps. Add the nutmeg, salt, and pepper to taste. Cook, stirring frequently, for about 15 minutes, or until the sauce thickens and becomes smooth and creamy.
Combine the pasta and sauces: Cook the penne in salted boiling water until just al dente, then drain. Toss the pasta with the béchamel sauce until well coated. Stir in half of the Bolognese meat sauce, half of the mozzarella, and half of the grated Parmesan cheese.
Assemble the pasta al forno: Preheat your oven to 375°F. Spread a layer of the remaining meat sauce over the bottom of a 9 × 12-inch oven-safe baking dish. Add the pasta mixture and spread it evenly. Top with the remaining meat sauce, mozzarella, and grated Parmesan cheese.
Bake: Cover the baking dish with foil and bake for 45 minutes. Remove the foil and continue baking for another 15 minutes, or until the cheese is melted, bubbly, and beginning to brown.
Rest and serve: Remove the pasta al forno from the oven and let it rest for a few minutes before serving. This allows the sauce to settle and makes the baked pasta easier to portion.