Combine squash, 1 1/2 teaspoons oil, 1/4 teaspoon salt, and 1/4 teaspoon pepper on a jelly-roll pan coated with cooking spray.
Bake at 425 for 24 minutes or until tender, stirring once.
Cook the pasta according to package directions, omitting salt and fat.
Drain pasta; keep warm.
Heat a medium saucepan over medium-high heat.
Add remaining 1 teaspoon oil to pan; swirl to coat.
Add onion and garlic; saut 3 minutes. Reduce heat to medium-low. Stir in 1/2 cup milk, remaining 1/4 teaspoon salt, and remaining 1/4 teaspoon pepper.
Combine remaining 1/2 cup milk, flour, and yolks in a small bowl, stirring with a whisk. Slowly add egg mixture to pan, stirring constantly with a whisk. Cook 5 minutes or until thickened, stirring frequently with a whisk.
Combine squash, pasta, and milk mixture in a large bowl; toss gently to coat.