Just speculating and opinionating, here, but...
German tanks were hardly slipshod products, far as I know. They were built in small numbers and much more like "Rolls" than "Ford-T" - much hand-work and fitting, less mass-production assembly-line stuff. The Germans were a bit "obsessive" and "perfectionist", as well as sometimes a bit overly complex and over-engineered regards the tank.
While they certainly had imperfections, and each tank (like each individual car) had its unique errors and issues, these probably were small-scale errors and not something like poorly-mounted "guess and by-gosh" fenders. The fenders were assemblies and needed to align with attachment fittings on the hull, etc. This not to say that all fenders were equally well-mounted, of course.
What MAY be the case (and I am in no way suggesting that this IS, but...) is that L and R fenders did vary in specific points and were not simply mirror - images of each other. One side MAY have had some cut-out or positioning that differed from the other. Maybe the kit is reflecting this as a historic accuracy? I don't know hardly anything about the Pz IV and its fenders, but that odd and ugly little Pz. II J is quite notable for having a set of 4 completely different fenders - each differed from the others in size and shape and attachment points! No mirror-images there!
Maybe you have checked this out by looking at other's "J builds" or searching Web stuff on the real thing? Do the kit instructions say or show anything that indicates this difference to be the real case and "intentional" for the kit? Have you seen or read any reviews or threads which came up with this question?
Bob