Boil the macaroni in salted water until just al dente. Drain and set aside.
Warm the olive oil in a large skillet over medium heat. Sauté onion and jalapeño until softened, 3–4 minutes.
Stir in the garlic and taco seasoning and cook 30 seconds to bloom the spices. Fold in corn and black beans; heat through. Transfer mixture to a bowl.
Melt the butter in the same pot over medium heat. Whisk in flour and cook 1–2 minutes, stirring, to form a blond roux.
Slowly whisk in the milk. Simmer, whisking, until thickened and smooth, 3–5 minutes.
Reduce heat to low. Stir in sour cream, cheddar, and Monterey Jack until melted and silky.
Fold in the diced tomatoes and green chiles. Add the cooked pasta and the bean-corn mixture; toss to coat.
Season with lime juice, salt, pepper, and hot sauce if using. Sprinkle with cilantro and serve warm.