Roast the Squash and Garlic: Preheat oven to 400°F (200°C). Place the cubed butternut squash onto a large rimmed baking sheet. Drizzle with 1 1/2 tablespoons olive oil, 1/2 teaspoon salt, and 1/4 teaspoon black pepper; toss to coat evenly. Slice the top 1/4-inch off the whole garlic head, drizzle with remaining 1/2 tablespoon olive oil, wrap tightly in aluminum foil, and place on the sheet. Roast for 30 to 35 minutes until the squash is tender and caramelized at the edges and the garlic cloves are golden and spreadably soft.
Sauté Aromatics: While the squash roasts, melt 2 tablespoons of butter in a large heavy Dutch oven over medium heat. Add the diced yellow onion, diced Granny Smith apple, chopped fresh sage, and 1/4 teaspoon salt. Sauté for 6 to 8 minutes until the onion and apple are tender and translucent.
Simmer Soup Foundation: Add the roasted caramelized squash into the Dutch oven. Squeeze the roasted garlic cloves directly out of their skins into the pot. Pour in the 4 cups of broth, ground ginger, nutmeg, cinnamon, and remaining salt and pepper. Bring to a gentle boil, then reduce heat to medium-low and simmer uncovered for 10 minutes.
Purée to Silky Perfection: Turn off the heat. Use an immersion stick blender directly in the pot (or carefully ladle in batches into a high-powered countertop blender) and blend on high speed for 2 to 3 minutes until completely velvety, smooth, and glossy.
Enrich with Cream: Stir in 1/2 cup of heavy cream. Return pot to low heat and simmer gently for 2 minutes to warm through. Taste and adjust seasoning with a pinch more sea salt or black pepper if desired.
Garnish & Serve: Ladle soup into warm bowls. Swirl a spoonful of cream and a drizzle of olive oil over each bowl. Top with crunchy roasted pepitas and fried sage leaves. Serve warm alongside crusty artisan sourdough bread!