In a large mixing bowl, toss the butternut squash, carrots, bell pepper, and onion with olive oil, granulated garlic, ground ginger, dried thyme, salt, and pepper until evenly coated.
Arrange the vegetables in a single layer in the air fryer basket; work in batches if needed to avoid crowding.
Air fry at 400°F for 20 minutes, shaking the basket halfway through for even roasting.
Transfer the roasted vegetables to a Dutch oven and add the vegetable broth.
Bring to a simmer over medium heat and cook for 10 minutes, until the vegetables are very tender.
Remove from heat and blend with an immersion blender until completely smooth.
Stir in the heavy cream and adjust seasoning with additional salt and pepper to taste.
Ladle into bowls and top with roasted pepitas, a dollop of crème fraîche, and chopped chives.