Preheat the oven to 400°F. Line a rimmed baking sheet with parchment paper and set aside.
Toss the butternut squash with 1 tablespoon of the oil and the thyme and sage. Spread into one even layer on the prepared baking sheet and roast until tender, about 25 to 35 minutes, stirring once halfway through cooking.
Meanwhile, in a pot, bring the broth to a simmer and keep warm.
In a large, deep skillet, warm the remaining 2 tablespoons of oil over medium heat. Add the onion and sauté until soft and translucent, about 5 to 6 minutes.
Add the rice and stir to combine. Cook for 2 to 3 minutes to toast the rice, stirring occasionally.
Add the wine and stir until absorbed, about 4 to 5 minutes.
Add ½ cup of warm broth and stir until absorbed. Continue adding broth ½ to 1 cup at a time until it's absorbed, stirring frequently, until the rice is creamy and tender yet still al dente. Add ½ teaspoon of salt once the rice is starting to get tender, after about 10 minutes or so. This whole process could take anywhere from 20 to 30 minutes. You may not use the full 6 cups of broth, but it's better to have too much than too little. Any leftover broth can be stored in an air-tight container in the fridge.
When the rice is al dente, add the nutritional yeast, remaining ½ teaspoon of salt, and black pepper, if using. Stir in the roasted butternut squash.
Garnish with fresh thyme and serve hot.