Just use the bolt stop and pull the bolt back until the round comes out.
I don't know about the round hitting the bolt.
I believe the case hitting the bolt is because atlas bottom metal is the longest coal bottom metal for tikka t3x right now and it’s just cut out a hair to far towards the trigger. So if your case is comingup the magazine just right the case hits the bolt a bit until I give it a smack...its most likely just my personal rifle but man it’s all so tight for room. I’ll figure out something sooner or later that works better.