Heat the oven to 375°F and lightly grease a 9x13-inch baking dish. Cook the spaghetti in salted water until just shy of al dente, then drain.
Heat the olive oil in a large skillet. Add the ground beef and onion and cook until the beef is deeply browned and the onion is tender. Add garlic, Italian seasoning, black pepper, red pepper flakes, salt, and tomato paste and cook for 1 minute.
Stir in the marinara and simmer for 5 minutes. In a large bowl, mix the cream cheese, sour cream, Parmesan, and 1 cup mozzarella until creamy.
Add the hot spaghetti to the cream cheese mixture and toss until coated. Fold in the beef marinara, then transfer everything to the baking dish. Top with remaining mozzarella and provolone.
Bake for 20–25 minutes until hot and the cheese is fully melted. Rest for 5 minutes, then finish with parsley before serving.