I sat on one of these at the international bike show earlier this year and spent some time giving it a careful once-over and one area that didn't impress me was the factory hard bags. Basically plastic with a sheet of metal over it to give the rugged look. There were a bunch of little dents in them just from having people get on and off the bike. The mounting clips looked to be cheap plastic too - not what you'd expect for an adventure style bike. I asked the salesperson about it and he admitted they are weak and his response was basically "well, you can always bungee it on the back if one falls off;" Granted, that has nothing to do with the mechanics or performance of the bikes - but to me it raises a red flag if KTM is willing to cheap out in this area.
Anywhere KTM can cut down weight they can. Scratches, that'll happen to any cases after the first fall. KTM spent a lot to make the bike as light as possible. You can get as heavy duty panniers as you like for this bike (Jessie's, Touratech, etc same makers that make the after market GS1200 stuff) but they'll weigh a ton. Performance wise I bet the KTM bags with metal only where needed will win.
Here is the Jessies system for the KTM, the strongest panniers made but weigh as much as a tank!