Preheat oven to 475 degrees. On a baking sheet layer the butternut squash and drizzle olive oil on top. Lightly salt and pepper, and add the nutmeg. Mix together and roast for 17-20 minutes, until tender.
Bring a large pot of water to a boil; add salt and penne and cook until al dente. Drain the pasta.
Heat 1/4 cup olive oil in a large skillet. Add the mushrooms and sauté for about 4-5 minutes. Add the garlic, ginger, and crushed pepper; cook for 2-3 minutes. Add the cilantro (reserve some for the garnish) and the stock; reduce heat to simmer.
Add the pasta to the mixture and stir, adding in 1 cup of cheese. Salt and pepper to taste.
Garnish the dish with 1 cup of cheese and the rest of the chopped cilantro.