Preheat the oven to 400 degrees F. Halve the squash lengthwise and scoop out the seeds. Wash the seeds and reserve.
Using 1 tablespoon of the olive oil, grease a glass baking dish. Place the squash in the dish cut-side down. Pierce the squash all over with a fork. Roast until very tender, 45 minutes. Let cool.
Heat a large heavy pot over medium-high heat and add the remaining 2 tablespoons olive oil. Add the onions, carrots and celery and saute until just tender, 10 minutes. Add the garlic and saute for 2 minutes. Scoop the butternut squash flesh into the pot and stir. Add the chicken broth and bring to a boil. Reduce the heat to low, cover the pot and simmer until the vegetables are very tender, about 30 minutes.
Meanwhile, heat a small pan over medium-low heat. Add the squash seeds and toast, stirring occasionally, until crunchy, about 30 minutes. Season the seeds heavily with salt. Set aside to cool.
Cool the soup slightly and then puree in batches in a blender until very smooth. Return to the pot and keep warm over medium-low heat. Mix in 2 teaspoons of the chipotle.
Mix the sour cream and remaining 1 teaspoon chipotle in a small bowl. Season the chipotle cream with salt and pepper.
Transfer the bisque to bowls. Top each with a dollop of chipotle sour cream and toasted butternut squash seeds.
When blending hot liquid, first let it cool for five minutes or so, then transfer it to a blender, filling only halfway. Put the lid on, leaving one corner open. Cover the lid with a kitchen towel to catch splatters, and pulse until smooth.