Heat the oven to 425 F, and grease two baking sheets with the coconut oil.
Slice the acorn and butternut squashes lengthwise (through the stem) and remove the seeds, and season the squash meat with salt and pepper. Place the squash halves facedown on the baking sheets. Arrange the carrots, onion and garlic around and in between the squash halves on the baking sheets, and bake for 40 minutes.
Allow the squash to cool slightly before handling.
Carefully scoop the flesh from the squash halves and add it to a high-powered blender. Transfer the carrots, onion, garlic, apple, butter, ginger, cinnamon and nutmeg to the blender.
Blend well and set aside.
In a medium saucepan over medium-high heat, bring the vegetable broth to a boil. Reduce the heat to medium and stir in the blended squash mixture until well incorporated. Cook the bisque for 5 minutes, then reduce the heat and simmer for 10 minutes.