Adjust an oven rack to the middle position and heat the oven to 400 degrees.

Bring 4 quarts of water to a boil in a Dutch oven over high heat.

Stir in 1 tablespoon salt and the macaroni; cook until al dente, about 5 minutes.

Reserve ¾ cup of the pasta water and drain the pasta. Transfer the pasta to a bowl and set aside.

Wipe the Dutch oven dry. Add 1 tablespoon of the oil and return to medium-high heat until shimmering.

Add the beef and cook, breaking up the pieces with a wooden spoon, until it is no longer pink and beginning to brown, 5 to 8 minutes.

Drain the beef through a colander, discarding the drippings, and set it aside.

Add the remaining 2 tablespoons oil to the Dutch oven and return to medium-high heat until shimmering.

Add the onions, red pepper, garlic, chili powder, and cumin; cook, stirring occasionally, until the vegetables are softened and beginning to brown, about 7 minutes.

Add the diced tomatoes, tomato puree, brown sugar, the reserved pasta water, and the drained beef; bring to a simmer and cook, stirring occasionally, until the flavors have melded, about 20 minutes.

Stir in the cooked pasta and season with salt and pepper to taste.

Pour into a 9 by 13-inch baking dish (or a shallow casserole dish of similar size) and sprinkle with the cheese.

Bake until the cheese is melted and browned, about 15 minutes.

Cool for 5 to 10 minutes before serving.