Preheat the oven to 425 degrees Fahrenheit. Place the halved peppers in a large baking dish or on a rimmed baking sheet lined with parchment paper. Drizzle 1 tablespoon olive oil over the peppers and sprinkle them with salt and pepper. Rub the oil all over both sides of the peppers, then arrange them cut sides facing up. Bake for 20 to 25 minutes, until the peppers are a little blistered around the edges and easily pierced through by a fork. Set aside.
In the meantime, bring a large pot of water to boil. Rinse the rice in a fine-mesh colander until the water runs clear. Add the rice to the boiling water and continue boiling, uncovered, for 30 minutes. Drain the remaining cooking water and return the rice to the pot. Set aside.
In a large skillet over medium heat, warm 2 tablespoons olive oil until shimmering. Add the onion and ? teaspoon of the salt. Cook, stirring often, until the onion is tender, about 5 minutes. Add the tomatoes and cook until they?re lightly squishy, another 5 minutes.
Add the cilantro, garlic, chili powder, and cumin. While stirring, cook until the garlic is fragrant, about 30 to 60 seconds.
Remove the skillet from the heat and add the rice, beans, lime juice, and about 10 twists of black pepper. Stir to combine, then season with additional salt (about ? teaspoon) and black pepper to taste.
To stuff the peppers, first pour off any excess juice pooled within the peppers. Stuff each pepper generously with the rice mixture (if the peppers were truly large, you should have just the right amount of filling). Top the peppers with the cheese.
Bake at 425 degrees Fahrenheit for 12 to 13 minutes, until the cheese is golden in spots. Serve warm with fresh cilantro leaves or any other garnishes of your choice.