Add olive oil to the inner pot of an Instant Pot. Turn on "Saute" mode. Add onion and cook until starting to get soft.
Add ground beef and cook and crumble it with a wooden spoon until no longer pink. Turn Instant Pot off.
Add Italian seasoning, salt, pepper, garlic powder, crushed red pepper flakes and tomato paste and stir.
Pour shells on top of ground beef mixture.
Pour pasta sauce and water on top of shells. Do not stir, but press shells down into liquid with the back of a spoon.
Place lid on Instant Pot and make sure valve is in "sealing" position. Set to Pressure Cook on HIGH for 5 minutes.
Do a manual pressure release and when the pin drops, remove the lid. Stir in Parmesan cheese, heavy cream, and cream cheese. Serve.