Toss the butternut squash, apples, 1/4 cup of the olive oil, salt, and pepper together and place, in a single layer, on a baking tray. Roast until cooked through and beginning to brown around the edges, about 20 minutes.
In a large pot, sauté the onions, garlic, ginger, salt, and pepper in 1/4 cup of olive oil, stirring regularly until softened and fragrant, about 10 minutes.
Add the butternut squash, apples, and white wine to the pot and stir everything together. Add the broth, bring to a boil, reduce the heat to low, and simmer partially covered for 30 minutes.
Cool slightly and, using an immersion blender, blend until smooth.
In a small sauce pan, heat 1/2 cup of the olive oil over high heat. Add the sage leaves and fry, flipping once, until crispy, about 2 minutes. Remove the sage to a paper towel. Whisk the Greek yogurt into the olive oil until fully combined.
Divide the soup among six bowls. Drizzle with the sage-oil-yogurt and garnish with a fried sage leaf.