If using fresh pumpkin or squash, preheat oven to 425F. Peel, seed and chop pumpkin or squash, coat with EVOO, salt and pepper, and roast to tender, 45 minutes. If using canned pumpkin pure, skip this step.
Heat 1 tablespoon EVOO in a soup pot over medium-high heat. Saut carrots and onions to tender, about 10 minutes. Season with nutmeg, cinnamon, coriander, cumin, paprika, a drizzle of honey, salt and pepper to taste. Toast spices, about 1 minute.
Add the carrots and onions along with the roasted pumpkin or squash to the bowl of a food processor and pure with a splash of stock. If using canned pumpkin, pure the onions and carrots together with some stock and stir in the canned pumpkin to combine.
Wipe out the soup pot and return to heat. Melt butter, whisk in flour then milk. Season with salt and pepper, and thicken to coat a spoon. Stir in cheese to melt, add chipotle and adobo sauce. Stir in remaining stock and squash or pumpkin pure. Let simmer to thicken soup.
Place a few crushed tortillas in shallow bowl and top with soup. Mix the tortillas into soup as you eat, garnish with toasted pumpkin seeds on top.