Preheat the oven to 350°F (175°C) and lightly grease a 9x13-inch baking dish with olive oil or non-stick spray.
Cook the gluten-free pasta according to the package directions until al dente. Drain, rinse briefly with hot water, place in a large bowl, toss with 1 tablespoon olive oil, and set aside.
In a large saucepan over medium heat, melt 4 tablespoons unsalted butter. Whisk in 1/4 cup gluten-free flour and cook 1 minute, stirring, to form a roux.
While whisking, slowly pour in 5 cups milk until smooth. Add 1 teaspoon onion powder, 1 teaspoon garlic powder, 1 teaspoon paprika, 1 teaspoon mustard powder, 1/4 teaspoon salt, and 1/4 teaspoon red pepper flakes (if using).
Bring the sauce to a gentle boil over medium heat, then simmer for about 2 minutes while whisking until slightly thickened.
Reduce heat to low and, if using, stir in 1/2 cup sour cream until combined. Add 2 cups sharp cheddar, 1 cup white Colby, and 1 cup Parmesan, stirring until the cheeses are fully melted and the sauce is smooth.
Pour the cheese sauce over the cooked pasta and stir gently to combine. Transfer the mixture to the prepared baking dish and spread evenly.
In a medium bowl, mix 1 1/2 cups gluten-free cracker crumbs with 6 tablespoons melted butter until evenly moistened.
Sprinkle 1 cup white Colby, 1 cup cheddar, and 1/2 cup Parmesan evenly over the pasta, then scatter the buttery cracker crumb mixture on top.
Bake uncovered in the preheated oven for 25–30 minutes, until the top is golden brown and the casserole is bubbly.
Remove from the oven and let rest 10–15 minutes before serving.