Heat the oven to 375°F. Set a large oven-safe Dutch oven over medium-high heat. Add the chorizo and cook 2 minutes to start rendering the fat, then add the ground beef and cook, breaking it up, until browned with crisped edges, 6–8 minutes. Spoon off excess fat if needed.
Push the meat to the sides and add the onion to the center. Cook until softened, about 3 minutes, then stir in the garlic for 30 seconds. Sprinkle in the chili seasoning and smoked paprika and stir for another 30 seconds to bloom the spices in the fat.
Pour in the tomatoes with their juices, add the diced chipotles plus 1–2 tablespoons of the adobo (to your heat preference), and fold in the pinto beans. Bring to a lively simmer, scrape up browned bits, then reduce to medium-low and cook 10–12 minutes to thicken. Season with salt to taste.
Meanwhile, boil the macaroni in well-salted water until about 2 minutes shy of al dente. Drain, reserving 1/2 cup of the pasta water.
Fold the drained pasta into the chili, then stir in 1 cup of the shredded cheddar until melted. If the mixture looks tight, loosen with a splash of reserved pasta water until saucy and glossy.
Smooth the top and scatter the remaining cheddar evenly. Transfer the pot to the oven and bake for 12 minutes, until bubbling. Switch the oven to broil and cook 1–2 minutes more to blister the cheese lightly; watch closely.
Rest 5 minutes so the casserole sets. Finish with the lime juice, give it a gentle stir, and serve hot.