Turn on a multi-functional pressure cooker (such as Instant Pot(R)) and select Saute function. Heat oil and add onion. Saute until translucent, about 2 minutes; be careful not to brown the onion. Move onion to the side of the pot. Add a layer of butternut squash to the bottom of the pot. Brown slightly, about 4 minutes. Add remaining butternut squash, curry powder, cinnamon, and nutmeg. Mix and continue cooking until fragrant, about 1 minute.
Pour broth and applesauce into the pot with the butternut squash mixture. Close and lock the lid; set knob to sealing. Select high pressure and set timer for 15 minutes. Allow 10 to 15 minutes for pressure to build.
Release pressure using the natural-release method according to manufacturer's instructions, 10 to 40 minutes. Unlock and remove lid.
Mix pumpkin puree and ghee into the pot with the soup. Blend with a stick blender. Add honey and salt. Mix thoroughly.