Preheat the oven to 350 degrees. Spray a 9 by 12 (or similar) baking dish with cooking spray.
Bring a large pot of heavily salted water to a boil. Cook the penne according to the package directions. Drain.
While the penne is cooking, make the sauce.
Heat the olive oil in a large skillet over medium-high heat. Add the onions and cook until softened, about 5 minutes. Add the garlic and cook, stirring, for 30 seconds. Add the sausage and mushrooms and cook until the sausage is fully cooked and the mushrooms have released their liquid, the liquid has evaporated, and the mushrooms have browned, about 10 minutes.
Add the pasta sauce, Italian seasoning, and red pepper flakes and bring to a simmer. Simmer, uncovered, for 20 minutes.
Add the penne to the sauce along with the tomatoes and ¼ cup Parmesan cheese. Stir to combine. Transfer to the prepared dish. Sprinkle the mozzarella and remaining Parmesan on top and bake for 25-30 minutes or until bubbly and beginning to brown around the edges. Sprinkle the parsley over the top and serve.