Arrange the pepper halves cut-side up on a nonstick baking sheet or regular baking sheet lined with parchment paper. Sprinkle the interiors with salt and pepper and drizzle with 2 tablespoons oil. Place the baking sheet in the center of the oven and roast until the peppers are juicy and somewhat softened and tender, 12 to 15 minutes. Remove from the oven.
Meanwhile, heat the remaining tablespoon oil in a large heavy-bottomed pot over medium heat. When the oil begins to smoke lightly, add the meat in a thin layer and sprinkle with salt and pepper. Cook, stirring with a wooden spoon, until the meat browns and is cooked through, 5 to 8 minutes. Remove the meat with a slotted spoon to a medium bowl. Stir the onions, garlic, chili powder and cumin into the pot with a sprinkle of salt. Stir to blend, then cook until the flavors meld together, 5 to 8 minutes. Add the tomatoes and simmer gently over medium heat until the tomatoes fall apart and the chili starts to thicken, 12 to 15 minutes. Add the meat back to the pot along with the beans and apple cider vinegar. Remove from the heat.
Fill each pepper about halfway with the couscous. Divide the chili among all the peppers, layering it on top of the couscous. Top with the cheese and return the baking sheet to the oven. Bake until piping hot and the cheese is melted, 20 to 25 minutes.
Green bell peppers work too. You could also use leftover rice in place of the couscous.