Bring a large pot of salted water to a boil and cook the pasta according to the package directions for al dente. Reserve 1 cup of pasta water.
Meanwhile, in a large deep skillet, cook the bacon over medium-high heat until fully cooked, about 5 to 6 minutes. Transfer the bacon to a paper towel-lined plate and leave the bacon grease in the pan.
Reduce heat to medium and add the butter and sage leaves to the pan with the bacon grease and cook for 2 minutes.
Discard the sage leaves and add in the garlic paste and cook for 1 minute, stirring continuously so you don't burn the garlic.
Add in the flour and cook for 1 minute until the mixture has thickened, stirring frequently.
Add in the butternut squash, chicken broth, milk, heavy cream, mustard powder, onion powder, salt, and black pepper and cook until the mixture reaches a simmer. Reduce the heat to medium-low and cover the skillet and continue to cook for 10 to 12 minutes until the butternut squash is tender, stirring occasionally.
Use an immersion blender to blend the mixture right in the pan OR you can very carefully transfer the mixture to a blender and blend until smooth.
Once blended, add in the cheddar and Parmesan cheeses and stir until melted, about 3 to 5 minutes.
Add the cooked and drained pasta and the butternut cheese sauce into a large pot and stir to combine.
Chop the bacon into small pieces and stir into the pasta and serve immediately.