Cook the pasta: Bring a large pot of salted water to a boil. Cook pasta to just shy of al dente according to package directions.
Reserve 1/2 cup pasta water, then drain.
Blend the high-protein base: In a blender, combine cottage cheese and Greek yogurt. Blend until completely smooth. Set aside.
Start the roux: In a large pot or deep skillet, melt butter over medium heat.
Whisk in flour and cook for 1 minute, stirring, until it smells toasty but not browned.
Add milk and seasonings: Slowly whisk in milk until smooth. Add garlic powder, mustard, salt, and pepper. Simmer 2–3 minutes, whisking, until slightly thickened.
Lower the heat and add cheeses: Reduce heat to low.
Whisk in the blended cottage cheese-yogurt mixture. Add cheddar and Parmesan in small handfuls, stirring until melted and smooth. If the sauce looks too thick, stir in a splash of reserved pasta water.
Combine: Add the drained pasta to the sauce and fold to coat.
If using add-ins like chicken or veggies, stir them in now. Warm through for 1–2 minutes.
Taste and adjust: Season with more salt and pepper as needed. If you want extra tang, add a small spoonful of Dijon or a squeeze of lemon.
Serve: Spoon into bowls.
Top with a sprinkle of Parmesan or a crack of black pepper. Enjoy hot.