Pre-heat the over to 425F and arrange a rack in the middle
Line a baking sheet with aluminum foil.Place the squash pieces cut-side up on the baking sheet. Melt 1 TBSP of ghee and brush all of it over the tops and insides of the squash halves. Season generously with salt and pepper. Roast until knife tender, about 50 minutes to 1 hour.
Meanwhile, peel, core and cut the apple into medium dice. Cut the onion into medium dice. Melt the remaining TBSP of ghee in a large saucepan or Dutch oven over medium heat. Add the apple, onion, and sage (optional) season with salt and pepper and cook, stirring occasionally, until softened, about 7 minutes. Remove the pan from the heat and set aside.
When the squash is ready, set the baking sheet on a wire rack until the squash is cool enough to handle. Using a large spoon, scoop the flesh into the saucepan with the sautéed apple and onions, discards the skins.
Add the broth, water and measured salt and pepper, stir to combine and bring to a boil over medium-high heat. Reduce the heat to medium low and simmer, stirring occasionally and breaking up any large pieces of squash until the flavours meld, about 15 minutes. Remove the pan from the heat and stir in the milk.
Using a blender, puree the soup in batches until smooth, removing the small cap (the poor lid) from the blender and covering the space with a kitchen towel (this allows steam to escape and prevents the blender lid from popping off). Alternatively, use an immersion blender.
Taste and season with salt and pepper as needed. Serve garnished with the pumpkin seeds for crunch.