Cook pasta according to box. Drain. Set aside.
In a medium saucepan, heat oil. Add onion and thyme. Cook for 2 - 4 minutes or until onions are soft. Add flour. Cook for 2 more minutes stirring constantly.
Whisk in broth and add steamed butternut squash. Bring to a boil, whisking for 5 minutes. It will start to thicken. Add evaporated milk, nutmeg and salt. Allow it to boil again, 3 - 5 minutes.
Optional: use an immersion blender to smooth the sauce, or transfer to a blender. This was imperative in our household. But if you don't have a blender, feel free to leave the bigger chunks of butternut squash in the sauce.
Turn off heat. Add cheese. Whisk until melted. The sauce will thicken as the cheese melts and it sits.
Add the pasta back to the cheese sauce. Stir to combine.