Don't most people carry their ipad pro's in some sort of laptop bag? Even with a cover, an ipad pro is a fragile and expensive piece of equipment to expose to bumps and bruises of commuting. Get a lightweight laptop bag and keep your pencil in that
That's good for carrying it outside, but I think the issue is when you are in the house or your workplace, and you are moving about with your iPad and Pencil. You can put your Pencil down in the living room, then forget to take it with you when you walk to the den. Then you have to search all over the house trying to remember where you put the Pencil.