Preheat the oven to 425 degrees. Mix the nutmeg, 1 teaspoon garlic and the sage in a bowl. Rub over the pork and season with salt and pepper.
Toss the squash, apples, onion, the remaining 1/2 teaspoon garlic, the honey mustard, and salt and pepper to taste in a bowl. Spread out on a long sheet of foil. Add the rosemary and 3 tablespoons butter, then bring the ends of the foil together and crimp to seal into a packet. Place the packet on a baking sheet and roast on the upper rack until tender, 30 to 35 minutes. Poke holes in the packet to release steam.
Meanwhile, heat a large ovenproof skillet over medium-high heat. Add the remaining 2 tablespoons butter, then brown the pork on all sides, about 8 minutes. Add 2 tablespoons water and scrape up any browned bits from the pan, then transfer the skillet to the lower oven rack and roast until a thermometer registers 150, about 15 minutes. Transfer the meat to a cutting board and let rest 5 minutes.
Return the skillet to medium heat. Add 1/2 cup water, scrape up any browned bits and simmer about 2 minutes. Slice the pork and drizzle with the pan juices. Serve with the squash and apples.