Preheat oven to 220°C (425°F). Spread squash cubes on a large rimmed baking sheet in a single layer. Drizzle with 2 tablespoons olive oil, season with salt and pepper, and toss to coat. Roast 28 to 32 minutes, turning once at 20 minutes, until deeply caramelized on the cut surfaces and fully tender.
While squash roasts, heat remaining 1 tablespoon olive oil in a large pot over medium heat. Cook the onion, stirring occasionally, for 8 to 10 minutes until soft and lightly golden. Add garlic and ginger, stir 90 seconds until fragrant.
Add cumin, coriander, nutmeg, and cayenne to the pot. Stir for 60 seconds until the spices smell toasted and aromatic in the oil.
Pour in the broth and bring to a gentle boil. Reduce heat and simmer 10 minutes.
Scrape the roasted squash off the baking sheet into the pot, including all caramelized bits. Simmer 5 more minutes.
Turn off heat. Blend in batches in a countertop blender on high speed for 90 seconds until completely smooth, filling each batch no more than halfway. Or use an immersion blender directly in the pot for 2 to 3 minutes.
Return blended soup to the pot over low heat. Stir in cream and butter. Heat gently until a steady simmer appears. Taste and adjust salt, pepper, and spices.
Ladle into warmed bowls. Garnish with a cream swirl, toasted pumpkin seeds, fresh thyme, and chili flakes. Serve immediately.
