Prepare the oven and dish. Preheat the oven to 350°F. Butter a deep 9-by-13-inch baking dish.
Cook the macaroni. Bring a large pot of salted water to a boil. Cook the macaroni 2 minutes less than the package’s al dente instructions. Drain well without rinsing.
Divide the cheese. Combine the shredded cheddar, Colby, and Monterey Jack. Reserve one-third for the topping and use the remaining two-thirds for the sauce.
Make the roux. While the pasta cooks, melt the butter in a large saucepan over medium heat. Whisk in the flour and cook for 1–2 minutes, whisking constantly. Keep it pale; do not let it brown.
Add the milk. Slowly whisk in the evaporated milk, followed by the whole milk, until smooth. Bring to a gentle simmer and cook for 3–5 minutes, stirring frequently, until the sauce lightly coats a spoon. It should remain pourable.
Season the sauce. Stir in the kosher salt, garlic powder, onion powder, dry mustard, black pepper, and half the paprika.
Melt in the cheese. Remove the saucepan from the heat. Whisk in the sour cream until smooth. Add the sauce portion of the cheese a handful at a time, stirring until melted before adding more.
Combine and top. Fold the drained macaroni into the cheese sauce. Transfer to the prepared baking dish without packing it down. Sprinkle evenly with the reserved cheese and remaining paprika.
Bake. Bake uncovered for 25–30 minutes, until bubbling around the edges and lightly golden on top. Begin checking at 20 minutes to avoid overbaking.
Rest and serve. Let stand for 10 minutes before serving. The sauce will thicken slightly as it rests while staying creamy.