You can see all the beltings the cases have done on the upper receiver to the rear of the ejection port and along the top of the ejection port I am with Jims summation that the rough chamber is holding the rounds and its taking more push from the rod to get the case moving hence the rounds are being slammed out as the bolt body literally takes off on the ejection cycle and causing the dents and scratchings on the cases. As Paul S noted.
If your unsure about polishing it take it to a gunsmith for peace of mind.
I have used (on a 303) 1200 grit Wet & Dry little bit of RP 40 and a rod with a slot in the top so you make a sort of flapper and away you go with a variable battery drill your only polishing not trying to remove scads of material slow & steady
Your only trying to get the majority of the chamber polished so no need to go into the neck section just the main body. try the original upper after the chamber polish then put the after market back on and see if the brass gets hammered when the cycle works as it should.