Preheat oven to 400°F (200°C) and line a large rimmed baking sheet with parchment paper.
Toss cubed butternut squash with 1 tablespoon olive oil, 1/2 teaspoon kosher salt, and black pepper. Spread in an even layer and roast for 20-25 minutes until tender and lightly browned at edges.
In a large Dutch oven or soup pot, heat remaining 1 tablespoon olive oil over medium heat. Add diced shallots and cook for 3-4 minutes until translucent. Add garlic, grated ginger, and chopped apples, sautéing for 3 minutes until fragrant.
Add roasted squash cubes, vegetable broth, ground nutmeg, cinnamon stick, and fresh thyme sprigs to pot. Bring to a gentle boil, then reduce heat, cover, and simmer for 10 minutes.
Remove cinnamon stick and thyme sprigs. Use an immersion stick blender to puree soup directly in pot until silky smooth and velvety.
Stir in coconut milk, pure maple syrup, and remaining 1/2 teaspoon kosher salt. Simmer for 2 minutes to meld flavors, then finish with a splash of fresh lemon juice.
Ladle hot soup into shallow bowls. Garnish with a swirl of coconut cream, crunchy roasted pepitas, and fresh thyme. Serve with warm crusty sourdough bread!