If I understand your question correctly, using the rear bag on a benchrest would decrease muzzle rise, and removing it (and increasing muzzle rise) will make the groups print higher. Someone here correct me if I am wrong, please
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If you are shooting targets this is not an issue, but if you are hunting you need to sight in and practice in field positions. I think it is not so much an issue of flexibility than knowing how you and the gun will do under different shooting conditions.