Fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the macaroni, and return to a boil. Cook the pasta uncovered, stirring occasionally, until the pasta has cooked through, but is still firm to the bite, about 8 minutes.
Drain well in a colander set in the sink.
Preheat oven to 350 degrees F (175 degrees C).
Spray a 9x13 inch baking dish with cooking spray, and place the macaroni into the bottom of the dish.
Heat milk in a saucepan until hot but not boiling.
Melt butter in a saucepan, and cook and stir the onion, garlic, and chipotle chiles until the onions are translucent, about 5 minutes.
Whisk in flour, 1 tablespoon at a time, and let cook for about 3 minutes, whisking constantly to avoid burning.
Whisk in the hot milk, 1/2 cup at a time, and stir in paprika, salt, and pepper. Bring the mixture to a simmer (do not boil), whisking constantly until thickened, about 2 minutes.
Whisk in the cheeses, about 1/2 cup at a time, and stir until the cheeses have melted and the sauce is thick and smooth.
Pour the sauce over the macaroni in the baking dish, and stir gently to combine. Cover the dish with foil.
Bake covered until the dish is bubbling and the macaroni has absorbed some of the sauce, about 40 minutes. Uncover, and bake until golden brown on the edges, 10 to 15 more minutes.
