Preheat oven to 350.
Toss cubed butternut squash in 1 tablespoon of oil and spread out squash on a baking sheet. Bake squash for 20-25 minutes, or until you can easily pierce the squash cubes with a fork.
While the squash is baking, using a large stock pot, cook the pasta according to package and set aside.
Add the cooked squash and 1/2 cup milk to a high-speed blender. Blend on med/med-high until all squash is pureed. Scrape down sides if needed.
In a large stock pot (you can use the one you cooked the noodles in) add in the remaining 2 cups of milk and shredded cheeses. Stir continuously until all cheese is melted. Add in the pureed butternut squash, onion powder, and salt. Mix until combined.
Add cooked noodles back to pot with the butternut squash and cheese. Mix until combined and then pour into a 2-2.5 qt. baking dish or 9x11 glass baking pan.
In a separate bowl, combine the almond flour, 1 tbsp. oil extra-virgin olive oil, and chopped sage. Sprinkle over macaroni.
Bake uncovered at 350 for 20-25 minutes, or until completely heated through. Sprinkle with additional fresh sage if you have some left over.