Preheat the oven to 350 degrees F. Butter a 9-by-13-inch baking dish and set aside.
Cook the pasta in boiling salted water until very al dente, about 3 minutes less than the box instructions (it will finish in the oven). Drain and set aside.
Add the milk and annatto to a 3-quart saucepan over medium-low heat and bring to a low simmer. Place 1 cup cheese snacks in the center of a double-layered square of cheesecloth. Gather the sides together to form a pouch and secure with kitchen twine. Put the pouch in the warm milk and steep for 5 minutes. Turn off the heat, then remove the pouch and discard.
Add the butter to a 6-quart Dutch oven and let melt, then add the flour to make a roux. Whisk until smooth, then cook until blonde in color, 2 to 3 minutes. Whisking vigorously, slowly add the milk mixture. Bring to a simmer, whisking constantly, then cook, whisking occasionally, about 2 minutes more. Add the cheeses and season with salt and pepper. Mix in the pasta until fully coated. Transfer the mac and cheese to the buttered baking dish.
Crush the remaining cup cheese snacks in a resealable bag using a rolling pin. Top the mac and cheese in an even layer with the crumbled hot cheese snacks and bake until bubbly and gooey, 15 to 20 minutes. Serve warm.