Preheat oven to 350°F. Line a baking sheet with foil.
Brush the squash halves with 1 tablespoon of the olive oil, sprinkle with salt, and place them skin side up onto the baking sheet. Bake for 50-60 minutes, until fork tender.
While the squash is baking, heat the other 2 tablespoons of olive oil in a large pot over medium heat. Add the onion and cook until translucent. Add the garlic, ginger, dried sage, and dried rosemary and cook for 1 minute.
Stir in the vegetable broth and bring to a boil. Turn off the heat and transfer the soup into a blender. Scoop the meat out of the baked butternut squash, place it into the blender, and blend until completely smooth (if you have an immersion blender you don't have to do this step, you can just blend everything in the pot). Transfer the soup back into the same pot and bring to a simmer. Turn of the heat and stir in the salt and pepper. Taste test for seasoning adjustments.
Serve garnished with fresh thyme.