Preheat the oven to 350°F (175°C) and lightly grease a 9x13 baking dish with olive oil or non-stick spray.
Cook the gluten-free pasta according to package directions until al dente. Drain, briefly run under hot water, toss with 1 tablespoon olive oil, and transfer to a large bowl.
In a large saucepan over medium heat, melt 4 tablespoons unsalted butter.
Add 1/4 cup gluten-free all-purpose flour to the melted butter and whisk until combined to form a smooth roux.
Gradually whisk in 5 cups milk, stirring constantly 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 (optional). Bring to a gentle boil, then simmer for about 2 minutes.
Reduce heat to low and, if using, stir in 1/2 cup sour cream until smooth.
Add 2 cups sharp cheddar, 1 cup white Colby, and 1 cup Parmesan to the sauce and stir until all the cheese is fully melted and the sauce is smooth.
Pour the cheese sauce over the cooked pasta in the large bowl and stir until evenly combined.
Transfer the macaroni mixture to the prepared baking dish and spread into an even layer.
In a medium bowl, combine 1½ cups gluten-free cracker crumbs with 6 tablespoons melted butter and stir with a fork until evenly moistened.
Sprinkle the remaining cheeses (1 cup white Colby, 1 cup cheddar, 1/2 cup Parmesan) evenly over the macaroni, then top with the buttery cracker crumb mixture.
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 for 10–15 minutes before serving.
