"What is the reason to cover the RotoPax with material??"
Mostly to not draw attention to the gas tank on the back of the bike. But makes it easier to carry with the handle. Some people don't like the big red gas can on their bike. You can also use straps to attach it to your panniers. There are loops on the bag that allow that. Keeps you from having to drill into your panniers for the rotopax mount.