Hmmm. If the barrel is out of index, the sights might look pretty odd when they are actually zeroed.
As the barrel rotates, so does the gas cylinder and operating rod guide. This is going to affect alignment, vibration pattern when cycling. In an extreme case, the engagement of the op. rod with the bolt is affected. None of this is going to help accuracy. If the barrel is slightly out of index, and you install a scope, you will likely never notice. If you are going to shoot with irons, you will notice it every time you bring the rifle up to aim.
Don't think it would be a safety issue.
Barrels being poorly indexed does not seem to be all that rare. Silly, because it is no harder to screw the barrel in to index than to screw it in out of index. Really suggests sloppy, indifferent assembly and inspection practices. Often all it takes is to bring the rifle to shoulder and aim it, and the accuracy of the indexing can be observed. There is no reason for rifles to be delivered at retail with obvious misalignment.