Roast the bell pepper over a gas flame, turning with tongs, or broil until the skin is blackened. Transfer to a bowl, cover and let cool. Peel, seed and chop the pepper.
Preheat the oven to 400 degrees F.
Spread the butternut squash on a rimmed baking sheet, drizzle lightly with EVOO, sprinkle with the nutmeg and cinnamon and season with salt and pepper. Roast until tender and browned at the edges, 20 to 25 minutes. Keep the oven on.
Meanwhile, combine the stock and sun-dried tomatoes in a small saucepan. Bring to a low simmer over medium heat and cook until very tender.
Heat 1 tablespoon EVOO in a soup pot over medium-high heat. Add the chorizo and cook until browned. Remove with a slotted spoon to a plate. Add the zucchini to the pot and cook until lightly browned, 6 to 8 minutes. Add the onions and cook until softened, 2 to 3 minutes, then add the roasted peppers.
Pour the sun-dried tomatoes and the cooking liquid into a food processor and add the Roasted Garlic Paste, cilantro, oregano and chipotle puree. Puree until smooth, then add the mixture to the chili and stir to combine. Add the beans, canned tomatoes, chorizo and roasted squash. Add enough water to thin the chili to the desired consistency.
Melt the butter in a small pan. Coarsely crumble the muffins on a baking sheet, then drizzle with the melted butter and sprinkle with seafood seasoning. Bake until browned.
Ladle the chili into shallow bowls and top with the Manchego cheese and crumbled muffins.
The chili can be covered and refrigerated for a make-ahead meal. Reheat over medium heat, stirring occasionally.
Roasted Garlic Paste:
Preheat the oven to 425 degrees F. Arrange the garlic in a cluster on a large piece of foil and drizzle with 1/4 cup EVOO. Wrap up the garlic in the foil to make a tightly sealed pouch. Roast until very tender, about 45 minutes. Let cool, then squeeze the garlic from the skins into a food processor. Add the remaining 3/4 cup EVOO and the honey and season with salt and pepper. Puree until smooth, then transfer to a small container. (Alternatively, you can mash the garlic paste with a fork instead of using a food processor.)