Preheat oven to 400°F.
Place butternut squash, onion, garlic cloves, and red bell pepper on a flat baking sheet in one layer. Moderately drizzle olive oil over the vegetables and toss in the thyme sprigs. Season with salt and pepper. Bake for 25-30 minutes or until butternut squash is tender. Toss halfway through.
While vegetables are roasting, cook chorizo in a skillet over medium-high heat until brown and crispy (about 8-10 minutes). Remove from skillet, drain off any excess oil, and place into a bowl.
Remove butternut squash mixture from the oven and place it into a Vitamix or blender with the chicken stock. Blend until smooth. Add more chicken stock if necessary to get a medium purée or your desired consistency. Pour soup from blender into a stock pot to warm thoroughly for about 20 minutes. Adjust salt and pepper.
Serve in individual bowls and garnish with the cooked chorizo, chiles, and pepitas.