Heat a large saucepan over medium heat, add the oil and when shimmering, add the scallions, bay leaves and cumin, and cook until softened about 3 minutes. Add the carrots, tomato paste and chipotle, and cook stirring until the carrots brown about 8 minutes.
Raise the heat to high and stir in the potatoes and squash, making sure they are well coated with the paste. Season with 1 tablespoon salt and freshly ground black pepper, to taste. Cook for about 5 minutes more. Pour in the broth and bring to a boil. Adjust the heat to maintain a gentle simmer, cover, and cook until the potato and the squash are tender, about 15 minutes. Remove and discard the bay leaves. Puree the soup until smooth with an immersion blender, or cool slightly and puree, in batches. in a jar blender. Keep warm.
Meanwhile, heat a medium skillet over medium-high heat. Add the butter, and when melted, stir in the bread cubes. Cook, tossing frequently, until golden brown, about 7 minutes. Sprinkle with lime zest and drizzle with the lime juice. Season with salt, to taste, and continue to toss and cook for another minute. Ladle the soup into serving bowls and scatter the croutons on top before serving.