I can vouch that when I worked at EB Games we had a shrink wrap machine. We would take the displayed copies of the games (gutted cases) re-fill them back up, shrink wrap them, and sell them as new. These were the games as employees we were allowed to take home to borrow.
Well, I can say without a doubt that is not how my game stop does things. As I said I've never not gotten a game from them that wasn't exactly as I could find it at BB, Wal-Mart, Target, etc.
I rarely PO games. I did PO 5 from Best Buy but only because they were giving me $100 credit if I did so.
At gamestop every game regardless of it being "new" or used they pulled a disk from locked cabinet. When I asked why they said is was for security reasons but they game was new they just open case and out disk in sleeve and put it in cabinet.
Well, I'd say if you PO games from Game Stop that might not be a problem. As I said its not been something I've run into but maybe the store I go to just has a classy manager running it.