I have modified nibconv so that it looks at what track it found when it tries to read track 18, so if it sees another track instead in the headers, it figures out how far off it is and extracts everything based on the offset. This only happens when decoding to D64, which is the only time this really matters.
The reason these images work on a real 1541 or emulation is that CBM DOS steps ahead and back one track and "aligns itself" to this kind of error when it can't read properly. Whatever track DOS then sees in the headers is the reality, regardless of the physical location of the track.
I've not ever seen this happen in all the thousands of disks I've imaged, but they have almost all been factory originals. I can see if you were archiving someone's private collection and their disk drive was out of alignment, this could happen.
C64 Preservation Project