Preheat oven to 400°F. Spread butternut squash out in an even, single layer on an aluminum foil lined baking sheet. Drizzle with 2 tablespoons olive oil and season generously with Kosher salt. Toss to coat. Roast squash in oven for approximately 25 minutes, until tender and easily pierced with a fork.
Meanwhile, heat remaining 1 tablespoon olive oil in a small skillet. Cook shallot, stirring occasionally, for 2 minutes. Stir in apple, rosemary, and sage, and season generously with Kosher salt. Cook for about 5 to 7 minutes, until apple is softened.
Combine rice with roasted butternut squash, apple mixture, dried cranberries, walnuts, and pepitas. Serve and devour.