Preheat the oven to 400 degrees F. Line a baking sheet with parchment paper.
In a large mixing bowl toss together the squash, onion, olive oil, ½ teaspoon sea salt, turmeric, cumin, paprika, cinnamon, allspice, and cayenne until well distributed. Transfer the squash mixture to the baking sheet and arrange in an even layer. Roast in the oven for 30 to 45 minutes, until the squash is tender and caramelized.
Remove from the oven and transfer to a medium Dutch oven. Add the potatoes, stock, and vinegar and bring to a boil. Simmer, partially covered, stirring once or twice, until the potatoes are tender, about 20 minutes.
Puree the soup using an immersion blender (or a regular blender). Taste for seasoning and add more salt as necessary. Ladle into bowls and garnish with a dollop of creme fraiche, a drizzle of olive oil, and the pepitas.