Preheat the oven to 400 degrees F. Fill a muffin tin with liners.
Bring a large pot of water with 2 tablespoons salt to a boil. Add the pasta and cook, stirring occasionally, until al dente, about 5 minutes. Drain well and set aside.
In a small saucepan over low heat, heat the milk.
In a large saucepan over low heat, melt the butter. Whisk in the flour and cook for 1 minute. Whisk in the warm milk (the mixture should start to thicken a bit) and cook for another minute. Add the butternut squash, garlic powder, egg yolk, 1/2 teaspoon salt and the pepper, and mix well. Remove from the heat, add 2 1/4 cups of the cheese and stir until the cheese has melted. Stir in the cooked pasta and toss to coat.
Fill each muffin cup with 1/3 cup of the pasta mixture. Sprinkle each with 1 teaspoon cheese. Bake until the sauce bubbles slightly and the tops begin to brown, 7 to 10 minutes. Let sit 5 minutes before serving.