Preheat the oven to 400°F. Arrange the pepper halves cut-side up in a large roasting pan or two baking dishes. Rub with ½ tbsp olive oil and sprinkle with ¼ tsp salt. Roast uncovered for 15 minutes. Carefully drain any liquid collected inside the peppers.
Meanwhile, heat the remaining ½ tbsp olive oil in a large skillet over medium-high heat. Add the beef and onion. Cook for 7–9 minutes, breaking up the beef, until browned and the onion softens. Drain excess grease.
Reduce the heat to medium. Add the garlic, Mexican seasoning, tomato paste, and remaining ¾ tsp salt. Cook, stirring, for 1 minute.
Stir in the salsa, water, cooked rice, and black beans. Simmer for 2–4 minutes, until hot with no loose liquid pooling in the skillet. Remove from heat and stir in 1 cup cheese, lime juice, and cilantro. Taste and adjust the salt.
Divide the filling among the pepper halves, gently packing it in and mounding slightly. Cover tightly with foil and bake for 15 minutes. If the peppers still feel too firm, continue baking covered until nearly tender.
Uncover and sprinkle with the remaining 1 cup cheese. Bake for 5–10 minutes, until the cheese melts and the peppers reach your preferred tenderness. Rest for 5 minutes before adding toppings and serving.
