Pre-heat the oven to 400°F and line two sheet pans.
Slice butternut squash in half lengthwise. Scoop out seeds with a spoon. Cut each butternut squash into 8 even wedges and place on a sheet pan. Drizzle with 1 tablespoon olive oil, 1 tablespoon maple syrup, and 1/4 teaspoon salt. Toss to coat. Roast for 40 minutes.
Chop the onions and apples into 2-inch chunks and place onto the second sheet pan with two whole, peeled garlic cloves. Drizzle with 1 tablespoon olive oil, ¼ teaspoon salt, and ¾ teaspoon black pepper. Toss to coat. Roast for 30-35 minutes.
Remove both sheet pans from the oven and cool slightly.
Scrape the skin from the roasted squash and discard. Add squash, onion, apples, garlic, to a blender. Blend until smooth and creamy. Add nutmeg, ginger, sage, paprika, cayenne pepper, and remaining ¾ teaspoon of salt to the blender. Drizzle in 2 teaspoons of olive oil and blend once more, until thoroughly smooth.
Serve topped with a squeeze of lemon juice and pepitas.
Store in the fridge for 3-4 days or freeze for 2-3 months.