I have experienced something like that in a Thompson Pennsylvania Hunter Flintlock. The ramrod moves easier in some areas of the barrel.
It doesn't affect the accuracy of my barrel, but then it is a blackpowder/patch and ball rifle and the apparent defect is much farther down the barrel than you describe. In mine I can compensate with a .003 thicker patch. And being classed as a 'Primitive', it is probably more like what they produced way back when.
If it was me, and I had a high powered rifle with a defect like you describe, I would contact CZ, just to make sure. You may experience 'blow-by' if the bore/bullet is too sloppy. You could end up losing accuracy and hitting power with a defect like that, if in fact it is defective.
I've heard of tools breaking during the rifling process and I've also heard of bores being out of center in other brands. All of which were taken care of through the manufacturer.