Heat the remaining 1 tablespoon olive oil in a large Dutch oven over medium heat. Add the diced onion and cook for 5–7 minutes until softened and translucent.
Stir in the chopped apples, garlic, and ginger. Cook for 3 minutes until fragrant.
Add the cinnamon, nutmeg, cloves, sage, and thyme. Stir and cook for 1 minute until the spices bloom and smell toasty.
Add the roasted squash to the pot along with the vegetable broth. Set aside ¼ cup of coconut milk for garnish, then stir in the rest. Add maple syrup, salt, and pepper.
Bring to a gentle boil, then reduce heat to low. Simmer, partially covered, for 20 minutes.
Using an immersion blender, blend the soup until completely smooth and velvety — about 2–3 minutes for an ultra-silky texture. Alternatively, blend in batches in a high-speed blender (vent the lid to release steam).
Stir in the apple cider vinegar to brighten the flavors. Taste and adjust salt. Thin with broth if too thick, or simmer uncovered to reduce if too thin.
Ladle generously into 4 bowls (about 16 oz each). Swirl in a spoonful of reserved coconut milk, top with toasted pepitas, crispy sage leaves, cracked pepper, and a drizzle of olive oil.