Preheat your oven to 400 F. Scatter the pumpkin seeds on a jelly roll pan and bake 5 minutes. Set aside.
Lightly grease a regular-sized baking sheet (a half sheet pan). In a small nonstick skillet, toast the cumin and coriander seeds over medium-low heat for 2-3 minutes or until fragrant. Transfer to a mortar, add the sage, and use the pestle to grind into a coarse powder.
Place the squash, ground spices, 2 ½ tbs oil, and salt to taste in a large bowl. Toss to evenly coat. Place on the prepared baking sheet, in a single layer, and roast 30 minutes. Add the apples and roast a further 20 minutes or until the squash and apple are tender.
Meanwhile, heat 2 tsp oil in a large stockpot. Add half the bacon and cook, stirring often, until browned and crispy. Remove with a slotted spoon and set aside on a paper towel lined plate.
Pour out enough bacon grease to leave about a tablespoon in the pot. Add the remaining half of the bacon and cook, stirring, until some fat has rendered, but it doesn’t need to be crispy. Add the onion and garlic and cook until the onion has cooked through but not browned. Shut off the heat. Transfer the squash and apples to the stockpot along with the chicken stock and half the goat cheese. Use your immersion blender to puree the soup until as smooth as possible. Simmer slightly for 6 to 8 minutes until thickened slightly. Taste for seasoning and add kosher salt and black pepper to taste.
Ladle into bowls, and garnish with the pumpkin seeds, the crisped reserved bacon, and the rest of the goat cheese.