Alignment of barrel threads in the receiver is huge if the rifle shoots consistently "a planet" over one side.
A barrel out of alignment, out of round etc isn't out of the question.
The rifle shoots off, and bad accuracy are two almost entirely separate subjects. Bad accuracy is often more difficult to troubleshoot.
Action bedding, or more accurately recoil lug bedding, caused my Savage Axis to shoot absurdly badly in a MDT chassis. Once I got that figured out it starting drilling holes on top of each other.
Start small and cheap like checking the scope bases/rings etc, then barrel nut like you've done. Often they're full of grinding compound or other grit.
A trick I used to use is to reverse one base, and then one ring to see if they're out. If not reverse then exchange front and back rings/bases.