Preheat the oven to 375°F. Bring a large pot of water to a rolling boil. Preheat a large skillet or Dutch oven over medium heat.
Add 1 tablespoon of olive oil, and the onion with a pinch of salt, and cook until starting to soften, about 4 minutes. Once the onion has softened, add in the tomato paste, minced garlic, garlic powder, onion powder, red pepper flakes, Italian seasoning, oregano, fennel seeds, and smoked paprika. Cook until the tomato paste begins to deepen in color, about 2-3 minutes.
Add the rest of the olive oil, followed by the ground beef, Italian sausage, and a big pinch of salt and pepper. Break the meat apart with a wooden spoon. Cook the meat until completely browned and cooked through. Do not drain!
Add crushed tomatoes, water, and basil to the skillet with a big pinch of salt. Bring the mixture to a simmer and let it cook for 5-10 minutes, until the sauce has slightly thickened. Remove from the heat, and remove about half of the meat sauce into a separate bowl and set aside.
Meanwhile, heavily salt the boiling pasta water. You will want about 2 tablespoons of kosher salt per pound of pasta. Cook the rigatoni until al dente. Make sure to reserve 1 cup of pasta water before draining.
Add the cooked pasta to the Dutch oven with the remaining sauce. Toss the mixture to combine, adding splashes of pasta water if necessary to help the sauce cling to the noodles. Place a layer of meat sauce on the bottom of the casserole dish, followed by a layer of rigatoni tossed in sauce.
Layer on some of the mozzarella cheese, some dollops of ricotta, and parmesan cheese. Continue layering noodles and cheese until all of the noodles are in the baking dish. Layer the rest of the meat sauce over top to help prevent the noodles from drying out while the pasta bakes.
Add a thick layer of the remaining ricotta, mozzarella cheese, and parmesan cheese. Bake the rigatoni in the preheated oven, uncovered, for 25-30 minutes, until the cheese is melted and bubbly. Broil for 2-3 minutes if desired to get the cheese to brown up. Allow the pasta to rest for about 10 minutes before digging in to make it easier to scoop out portions.
Store leftover pasta airtight container or covered with plastic wrap after allowing it to cool at room temperature. To freeze, allow to cool completely, then transfer to a freezer-safe container for up to 3 months. Defrost overnight in the fridge, and reheat in the oven, air fryer, or gently in the microwave.