Cook the penne pasta in a large pot of salted water according to package directions until al dente. Drain and set aside.
In the same pot, melt the butter over medium heat. Add the diced onions and sauté for 4-5 minutes until softened.
Stir in the tomato paste and minced garlic, cooking for an additional 2 minutes.
Reduce the heat to low and pour in the spaghetti sauce, heavy cream, and red pepper flakes (if using). Simmer gently. Season with salt and pepper to taste.
Return the cooked pasta to the pot and toss until evenly coated in the sauce.
Sprinkle the mozzarella and Parmesan cheese on top. Cover with a lid and let it sit for 2-3 minutes, or until the cheese is melted.
Serve warm with crusty bread.