Bring a large pot of salted water to a boil. Add pasta and cook according to package directions.
While the pasta cooks, heat a saucepan or pot over medium heat. Add the butter. Allow the butter to melt and brown, about 2 to 3 minutes. Then whisk in the flour and cook 1 to 2 minutes until it just starts to bubble and turns a golden color. Make sure to whisk constantly to avoid clumping.
Gradually pour in the half and half while whisking until smooth. Continue cooking and whisking until the sauce thickens up like a bechamel. Then add the butternut squash puree, dry mustard powder, smoked paprika, garlic powder, salt, black pepper, sage, thyme, nutmeg, onion powder, and cayenne powder. Whisk together.
Reduce the heat to low or turn off the heat entirely and add all the cheeses. Whisk together until all the cheese is melted and the sauce is completely smooth. Taste and adjust anything to your liking.
Once the pasta is done cooking, drain it and toss it into the sauce. Mix together and serve warm!