Prepare the pasta water. While the acorn squash bakes, gather your ingredients for the roux. Place a large pot of salted water on the stovetop over medium heat and bring to a boil in preparation for cooking the gluten free protein pasta.
Heat the butter and liquids. In a large, deep saucepan, add the butter, non-dairy or lactose-free milk, and broth. Bring to a simmer, stirring to help melt the butter and combine the ingredients.
Add the flour. Once the butter is fully melted, add the gluten free 1:1 flour, one tablespoon at a time, whisking vigorously to combine.
Thicken the roux. The mixture will begin to thicken. Continue whisking, smoothing out any remaining clumps of flour.
Add the cheese and spices. Add the cream cheese and shredded cheese, continuing to whisk until smooth. Once the cheese is fully incorporated, add the salt, nutmeg, mustard seed, paprika, and optional turmeric. Whisk until everything is combined and the sauce is smooth.
Cook the pasta. By now, your pasta water should be at a rolling boil. Add the entire box of gluten free protein pasta and cook according to the package instructions, until al dente. Cooking times will vary depending on the pasta used.
Keep the sauce warm. Continue whisking the cheese sauce over low heat while the pasta cooks to prevent it from thickening or solidifying.
Combine the pasta and cheese sauce. As soon as the pasta is ready, transfer it directly into the cheese mixture using a slotted spoon. Do not drain the pasta first; you'll want a little of the pasta water to transfer into the cheese mixture to thin it out slightly. Gently fold the pasta into the cheese sauce until evenly coated.