Preheat your oven to 400°F (200°C). Brush the cut sides of the butternut squash with 1 tablespoon of olive oil and season with salt and pepper. Place the squash halves cut-side down on a baking sheet lined with parchment paper. Roast for 35-45 minutes, or until the flesh is tender and easily pierced with a fork. While the squash is roasting, heat the remaining tablespoon of olive oil in a large skillet over medium heat. Add the sausage and cook, breaking it into crumbles, until browned and fully cooked. Add the onion and cook until softened, about 3-4 minutes. Stir in the garlic, thyme, red pepper flakes, and spinach (if using) and cook for 1-2 minutes until fragrant and the spinach is wilted. Remove the skillet from heat and stir in the breadcrumbs and Parmesan cheese. Once the squash is done roasting, carefully scoop out some of the flesh from each half, leaving a border to help them hold their shape. Chop the scooped-out squash and mix it into the sausage mixture. Turn the squash halves cut-side up and fill them generously with the sausage mixture. Sprinkle additional Parmesan cheese on top if desired. Return the stuffed squash to the oven and bake for another 10-15 minutes, or until the filling is golden and heated through. Garnish with fresh parsley and serve warm.