The scratches are being put on the bullet when you are extracting it from the chamber. If you shoot the bullet, it goes out the barrel and CAN'T get scratched....silly.
And, if you are so concerned about any deformations to the bullet causing accuracy issues, don't use a semi-auto in the first place. The bolt pushing the round out of the magazine, up the feed ramps, and into the chamber will ALWAYS "potentially" cause slight deformations to the bullet and/or case. If you want absolutely NO possible dings to your rounds during the violent action known as chambering in a semi-auto, it ain't gonna happen. You need to be using a bolt action and loading one round at a time directly into the chamber so that it doesn't drag/rub/slide against anything other than the chamber walls when chambering the round.
And, if you are so concerned about any deformations to the bullet causing accuracy issues, don't use a semi-auto in the first place. The bolt pushing the round out of the magazine, up the feed ramps, and into the chamber will ALWAYS "potentially" cause slight deformations to the bullet and/or case. If you want absolutely NO possible dings to your rounds during the violent action known as chambering in a semi-auto, it ain't gonna happen. You need to be using a bolt action and loading one round at a time directly into the chamber so that it doesn't drag/rub/slide against anything other than the chamber walls when chambering the round.