To make your cheese sauce, melt dairy-free butter in a small pan. Wait for butter to fully melt. Then add flour. Whisk vigorously until combined.
Start gradually and slowly (e.g, only ¼ cup at once) adding your plant milk. At the same time, keep whisking.
Once you’ve added all your plant milk, keep whisking some more. The sauce should be perfectly smooth with no lumps.
Lastly, add all your seasoning and shredded vegan cheese to the hot pan. Keep whisking on medium-heat until everything has dissolved and thickened to almost gravy-like consistency (but less thick).
Boil your pasta - make sure to boil about 3-4 minutes less than regularly. Your pasta needs to be al dente before going into the oven.
Once your pasta is cooked (do not overcook), reserve ¼ cup of pasta water. Drain the rest. Add your pasta to a large baking tray.
Pour over your cheese sauce and pasta water. Add butternut squash. Mix well and add some more smoked paprika and sage if desired. Top off with ground almonds and nutritional yeast.
Bake in the oven at 180°C/35°F for 25 minutes. Serve hot or store in an airtight container for later.