Add rice and water to a saucepan and bring to a boil over high heat. Reduce the heat to medium-low, cover, and simmer for 20–25 minutes until the rice is tender and the liquid is absorbed. Set aside.
Preheat the oven to 375°F (190°C).
Heat olive oil in a skillet over medium heat. Add onion and cook until softened, about 5 minutes. Transfer half of the cooked onion to a large bowl and reserve.
Add marinara sauce, beef broth, balsamic vinegar, and red pepper flakes to the skillet with the remaining onion. Stir and cook for about 1 minute.
Pour the sauce mixture into a 9×13-inch baking dish and spread evenly.
In the bowl with the reserved onion, combine ground beef, Italian sausage, diced tomatoes, parsley, garlic, salt, black pepper, and cayenne pepper. Mix until well combined.
Stir the cooked rice and Parmigiano-Reggiano cheese into the meat mixture.
Fill each halved green bell pepper with the beef and rice mixture, packing it gently into the peppers.
Arrange the stuffed pepper halves in the baking dish over the tomato sauce. Sprinkle additional Parmigiano-Reggiano over the tops.
Cover the baking dish with aluminum foil and bake for 45 minutes.
Remove the foil and continue baking for 20–25 minutes, until the meat is fully cooked, the peppers are tender, and the cheese is lightly browned.
Serve warm with extra sauce from the baking dish.