Bring a large pot of salted water to a boil. Add the whole wheat elbow macaroni and cook according to package instructions until al dente, about 7-8 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium-high heat. Add the finely chopped onion and cook for 3-4 minutes until softened.
Add the minced garlic to the skillet and cook for 30 seconds until fragrant.
Add the lean ground beef to the skillet. Cook, breaking it apart with a spoon, until browned and cooked through, about 6-8 minutes. Drain any excess fat if necessary.
Sprinkle the all-purpose flour over the cooked ground beef mixture and stir well to coat. Cook for 1 minute to remove the raw flour taste.
Gradually pour in the low-sodium chicken broth and milk while stirring continuously to avoid lumps. Bring the mixture to a simmer and cook until slightly thickened, about 3-4 minutes.
Reduce the heat to low and stir in the shredded sharp cheddar cheese and shredded mozzarella cheese until fully melted and smooth.
Add the smoked paprika, black pepper, salt, ground mustard, and crushed red pepper flakes (if using). Stir to combine all seasonings evenly.
Add the cooked macaroni to the cheese and ground beef sauce. Stir gently to combine and heat through for 2 minutes.
Remove from heat and sprinkle the grated Parmesan cheese on top before serving.