Step 1:

Fill a large pot with water, add salt, and bring it to a boil over high heat.

Step 2:

In a large skillet, combine the frozen butternut squash and 1/4 cup water over medium-high heat. Cover and cook, stirring occasionally, until the squash is tender, about 5 to 7 minutes. Uncover and continue to stir until the liquid evaporates, approximately 2 to 3 minutes.

Step 3:

Stir in the butter, 1/2 teaspoon salt, and 1/4 teaspoon black pepper until the butter melts. Add the flour, stirring continuously to blend. Cook, stirring constantly, for 2 to 3 minutes until the mixture thickens and the flour is cooked through. Gradually pour in the milk, stirring all the while. Incorporate the garlic powder, a pinch of cayenne pepper, and fresh thyme. Bring the mixture to a gentle simmer. Add the cheddar and goat cheese, stirring until fully melted. Remove from heat and let it cool slightly.

Step 4:

Add the pasta to the pot of boiling water and cook until just shy of al dente, about 3 minutes less than the package instructions indicate. Drain, reserving 1/2 cup of the pasta water, and return the pasta to the pot.

Step 5:

Transfer the squash mixture to a blender and puree until smooth. The resulting sauce should yield just over 4 cups.

Step 6:

Place the pot with the drained pasta over medium-low heat. Gradually stir in the butternut squash sauce until the pasta is evenly coated. Let the mixture cool for about 5 minutes to thicken. If the sauce seems too thick, add reserved pasta water in small increments until you reach your desired consistency.