Fill a large pot with lightly salted water and bring to a rolling boil. Stir in macaroni and return to a boil. Cook macaroni uncovered, stirring occasionally, until tender yet firm to the bite, about 8 minutes. Drain well in a colander set in the sink.

Preheat the oven to 350 degrees F (175 degrees C). Lightly coat a 9x13-inch baking dish with cooking spray.

Place macaroni into prepared baking dish. Meanwhile, heat milk in a saucepan until hot but not boiling.

Melt butter in a separate saucepan. Add onion, garlic, and chipotles; cook and stir until onion translucent, about 5 minutes. Whisk in flour, 1 tablespoon at a time; cook about 3 minutes, whisking constantly to avoid burning. Whisk in hot milk, 1/2 cup at a time. Stir in paprika; season with salt and pepper. Bring mixture to a simmer (do not boil), whisking constantly until thickened, about 2 minutes. Whisk in Cheddar and Monterey Jack, 1/2 cup at a time; stir until cheese melted and sauce thick and smooth.

Pour sauce over macaroni; stir to combine. Cover dish with foil.

Bake covered until bubbling and macaroni has absorbed some sauce, about 40 minutes. Uncover; continue baking until golden brown on edges, 10 to 15 minutes more.