1. Preheat oven to 350F. Split squash in half lengthwise. With spoon, scrape out seeds and fibers from cavity. Season cut side of squash with 1 tsp. salt; place flesh side down in a lightly buttered baking dish or a 15x10x1-inch baking pan lined with parchment paper.
2. Add in 1/2 cup water to baking pan. Bake 1 to 1-1/2 hours, until skin is browned and flesh is tender when pierced with knife. Remove from oven; let rest until cool enough to handle. Scoop out flesh; discard skin.
3. In large saucepan or Dutch oven, heat butter until foaming. Add diced onion and season with 1/2 teaspoon salt. Sprinkle thyme over onions. Add bay leaf. Cook over medium heat, stirring often, until the onions are tender and translucent (do not allow to color), about 10 minutes.
4. Add squash. Season with additional salt and pepper. Cooking 5 minutes, stirring often.
5. Add broth; bring to simmer. Simmer, uncovered, 20 minutes, stirring occasionally. Season to taste. Remove bay leaf. Stir in honey. Cool slightly. Puree soup, one half at a time, in blender or food processor.
6.Stir in 1/4 cup cream and 1/4 tsp. grated nutmeg. Taste for seasoning, add salt, pepper, and honey as needed. Cool slightly. Transfer to a storage container; cover and chill up to 2 days.
7.To reheat soup: Cook over medium heat, stirring occasionally until heated through. Drizzle with remaining cream and sprinkle with remaining nutmeg.
To serve right away: Omit chilling- just reheat after pureeing; drizzle with cream and sprinkle with nutmeg after heating through.