Roast the squash: Preheat your oven to 180°C (350°F). Place the squash halves, cut-side up, on a large baking tray. Drizzle with 1 tablespoon of olive oil and season with salt and pepper. Roast for 30 minutes, or until the flesh is starting to soften.
Prepare the spicy filling: While the squash is roasting, heat the remaining 2 tablespoons of olive oil in a frying pan over medium heat. Add the red onion, red pepper, garlic, and chili (if using), and fry until the vegetables are soft, about 5-7 minutes. Stir in the spinach and cook for a further minute until wilted. Remove the pan from the heat.
Add heat and sweetness: Stir half of the goat's cheese, the honey, and the crushed red pepper flakes into the vegetable mixture. Season well with salt and pepper to taste.
Stuff the squash: Remove the partially roasted squash from the oven. Fill the hollows of each squash half generously with the vegetable and goat's cheese mixture.
Final bake: Return the stuffed squash to the oven and bake for another 15 minutes, or until the squash is completely tender and the cheese is melted and lightly browned.
Garnish and serve: Remove from the oven. For extra crunch, scatter with pumpkin seeds or walnuts, and drizzle with a little extra honey and red pepper flakes if desired. Serve warm.