Preheat the oven to 350°F. Add the cubed squash, sweet potatoes, and garlic bulbs to a sheet pan. Drizzle with olive oil and honey, sprinkle with the seasonings and salt, and toss to coat.
Roast for 35–45 minutes, until the squash and sweet potatoes are softened and lightly toasted and the garlic is soft.
While the vegetables roast, melt the butter in a large pot over medium heat. Add the onion and cook until translucent, about 5–7 minutes.
Squeeze the roasted garlic cloves out of their skins and into the pot. Stir to combine with the onion.
Add the roasted squash and sweet potatoes to the pot along with 2 cups of chicken broth.
Blend until smooth with an immersion blender, or carefully transfer to a blender in batches. Add more broth a little at a time while blending until the soup reaches your desired consistency.
Stir in the Better Than Bouillon and half and half. Simmer over medium-low heat for about 10 minutes, until heated through.
Ladle into bowls and top with chili flakes and fresh thyme.