Bring a large pot of water to a boil. Cook the macaroni according to the package instructions. Drain and set aside.
Heat the butter in a large saucepan over medium heat. Add the crushed red pepper, jalapeno, garlic and onion and cook, stirring, until the veggies have softened, about 5 minutes. Add the milk and heat until starting to bubble around the edges. Add the processed cheese and stir until melted. Add the Monterey Jack and pepper jack cheeses, pepper, kosher salt, seasoned salt and hot sauce to taste. Stir until the cheese is melted. Taste and adjust the seasoning. Add a splash of milk if the sauce seems too thick. Fold in the cooked macaroni and serve.
Reheating instructions: Preheat the oven to 350 degrees F. Put the mac and cheese in a baking dish, cover with foil and heat until warmed through, about 25 minutes.