Bring 4 quarts of heavily salted water to a rolling boil. Cook penne according to package instructions until al dente. Reserve 120ml of pasta cooking water, then drain.
In a large heavy-bottomed skillet, heat 1 tbsp olive oil over medium-high heat. Add butternut squash cubes and sauté for 8-10 minutes until tender and caramelized. Remove and set aside.
In the same skillet, add the remaining olive oil and the bulk sausage. Cook while breaking into 1/2-inch crumbles until the internal temperature reaches 160°F (71°C).
Add the diced onion to the sausage crumbles. Sauté for 4 minutes until translucent. Add minced garlic, sage, and nutmeg, cooking for 60 seconds until fragrant.
Deglaze the skillet with chicken broth, using a wooden spoon to scrape the fond from the bottom of the pan.
Reduce heat to medium-low and stir in the heavy cream. Simmer for 3 minutes. Slowly whisk in the Parmesan cheese until the sauce is emulsified and thickened.
Incorporate the cooked pasta and sautéed squash into the sauce. Toss to coat, adding the reserved pasta water 1 tbsp at a time to adjust viscosity.
Season with salt and black pepper. Serve immediately while internal temperature is above 140°F (60°C).