Preheat the oven to 375°F (190°C). Have a 9x13-inch baking dish ready.
Prepare the peppers by slicing off the tops about 1/2 inch below the stem. Reserve the tops. Remove the cores and seeds, then trim a very thin slice from the bottom of each pepper if needed so it can stand upright. Make a few tiny holes in the bottom of each pepper to help excess juices escape.
Add 2 1/2 cups of tomato sauce to the baking dish. Scatter the sliced onion over the sauce, then pour in the beef broth and sprinkle with red pepper flakes. Spread everything evenly across the bottom.
Arrange the prepared peppers upright in the baking dish.
In a large bowl, combine the ground beef, cooked rice, Parmesan cheese, 2 tablespoons of tomato sauce, chopped parsley, minced garlic, salt, and black pepper. Mix gently until the ingredients are evenly incorporated without overworking the meat.
Spoon the filling into each pepper, leaving a little room at the top. Add a small spoonful of the remaining tomato sauce over the filling and place the reserved pepper tops back on.
Loosely cover the peppers with parchment paper, then tightly cover the baking dish with aluminum foil. Place the dish on a baking sheet to catch any bubbling sauce.
Bake for about 60 minutes, or until the peppers begin to soften and the filling is nearly cooked through.
Carefully remove the foil and parchment. Return the dish to the oven and bake uncovered for another 20–30 minutes, until the beef is fully cooked and the peppers are tender.
Finish the beef and rice stuffed peppers with fresh parsley and spoon some of the flavorful pan juices over each pepper before serving.