Preheat oven to 400°. Place butternut and banana squash, cut side up, in a 12- by 17-in. roasting pan (or divide squash evenly between two 9- by 13-in. pans). Add boiling water to pan to a depth of 1/2 in.; cover tightly with foil. Bake until squash is very soft when pierced, about 1 hour. Remove squash from pan, drain briefly, and set aside until cool enough to handle.
Meanwhile, place chipotle chile in a small bowl; add boiling water to cover. Let stand 5 minutes; drain.
Combine chipotle, broth, ancho chile powder, and habanero in a 5- to 6-qt. pan over high heat. Bring to a boil, cover, and simmer 20 minutes. With a slotted spoon, remove chipotle and habanero chiles; discard.
Scrape cooked squash from rind. Whirl squash in batches in a blender or food processor until very smooth. Add squash purée and lime juice to broth mixture.
Add zucchini to soup and stir often over medium-high heat until soup simmers and zucchini are tender when pierced, about 10 minutes (20 minutes if reheating).
Ladle soup into 1 large bowl or individual serving bowls. Top decoratively with chile garnish and sour cream, or offer both to add to taste.
Make ahead: Cover and chill up to 1 day.
Note: Nutritional analysis is per 1-cup serving.