Bring a large pot of well-salted water to boil over high heat.2 Once the salted water begins to boil, add the dry shells pasta and cook according to package directions minus three minutes from al dente. When the pasta is almost done, reserve about a cup of the pasta water. Drain the pasta in a colander set in the kitchen sink.
In a large skillet with a lid, set over medium-high heat, combine the frozen butternut squash and ¼ cup of water. Place the lid on the pan and cook, stirring occasionally, for 5 to 7 minutes. Then, uncover and cook for 2 to 3 minutes, stirring constantly, until all of the water has evaporated.
Add cubed unsalted butter, freshly ground black pepper, and Kosher salt and stir until the butter is melted.
Then, add the all-purpose flour and stir to incorporate. Cook, stirring constantly, until the squash mixture has thickened, for about 2 to 3 minutes.
Gradually add the milk, about ½ a cup at a time, stirring constantly, until all of the milk has been incorporated.
Add the freshly minced thyme, garlic powder, and cayenne pepper, then bring to a simmer.
Add the goat cheese and extra sharp cheddar cheese, then stir constantly until all of the cheese is melted and well incorporated. Remove from the heat and allow to cool for about five minutes.
When the sauce mixture has cooled slightly, transfer it to a large four-cup measuring cup and clean the pan to ensure none of the chunky sauce mixture remains. Then, process the sauce in the blender in two batches until it's smooth and creamy. Return the first batch to the cleaned pan, then set the pan over medium-low heat. Leave the second batch in the blender until ready to incorporate it with the pasta.
Add the drained pasta to the sauce in the pan and stir the pasta into the sauce. Add the remaining sauce and stir so the all the pasta is well coated. Ladle in about ½ cup of the reserved pasta water and stir it into the Mac & Cheese. Remove the pan from the heat and let it cool for about five minutes. If the sauce is too thick, add some of the remaining water until the desired consistency is reached.
Yield 8 servings