Heat oven to 425°F. In a large bowl, toss the squash cubes with 1 tablespoon of oil and a large pinch of salt. Pour onto a baking sheet, spread to a single layer, then roast for 20 - 30 minutes, or until soft, stirring occasionally to brown them evenly.
While the squash is baking, bring a large pot of water to a boil; add the penne and cook, according to package directions, until al dente. Remove ⅔ cup of the cooking liquid. Drain the pasta and set aside.
Place half of the roasted squash into a blender or food processor, along with half of the reserved cooking liquid, process until smooth. It should look like thick tomato sauce. Add additional reserved cooking liquid until desired consistency is reached.
Meanwhile, in a large skillet, large enough to hold the mushrooms without crowding, (you can later use this for the pasta, so pick a large skillet) heat 1 tablespoon oil along with 1 teaspoon butter, when hot, add the mushrooms and cook until lightly browned and tender. In another small skillet, heat the remaining 2 teaspoons butter over medium heat, when hot, add the sliced sage leaves, cook until the leaves and butter are lightly browned - do not burn the butter.
Remove the mushrooms from the skillet and set aside. Heat the remaining tablespoon of oil, add the shallot and sauté until tender, about 2 - 3 minutes, add the squash puree and roasted squash cubes; cook until hot. Add the drained pasta and mushrooms; toss until well heated and coated with the sauce. Add more pasta water if the sauce seems too thick. Divide the pasta and squash into 4 wide bowls. Spoon the browned sage butter and leaves evenly over the top. Finish with grated parmesan and parsley, if desired. Season with freshly ground pepper.