Preheat the oven to 425°F (220°C) and simultaneously bring a large pot of water to a boil, sufficient to submerge the bell peppers.
Prepare the bell peppers by rinsing, slicing off the tops, and hollowing out the interiors. If necessary, shave a thin slice from the bottoms to help them stand upright. Chop the pepper tops (excluding stems) to sauté with the onions later.
Blanch the hollowed peppers in boiling water for about 5 minutes to lightly soften them. Alternatively, roast them in the oven for 20 minutes instead.
Transfer the softened peppers to a baking dish that has been lightly coated with oil.
In a large skillet over medium heat, warm the olive oil and sauté the onion, chopped pepper tops, and jalapeño for 5 minutes until they begin to soften.
Incorporate the garlic and cook for another minute until aromatic.
Introduce the ground beef to the skillet, cooking it through while crumbling it apart, about 5-6 minutes.
Fold in the fire roasted tomatoes, dried herbs, paprika, and the cooked rice. Stir to blend thoroughly, then remove from heat.
Mix in half of the shredded cheese to integrate with the filling.
Generously fill each pepper with the prepared meat mixture and sprinkle the remaining cheese over the top of each one.
Bake in the preheated oven for 15-20 minutes, until the peppers reach your desired tenderness and the cheese on top is golden and bubbling.
Allow to cool briefly, then garnish with chopped parsley and red pepper flakes before serving.