Racking changes the appearance of the roof where you can see the shingle laid in a rack. The staggered way hides the stagger a little better. You can a clear staggered not straight up and down rack pattern in your shingles. You are looking not going to change the color by moving the shingles around, they don't put that kind of technology into shingle granules. You would just be seeing what you want to see.This issue is not your fault, nor the contractors. Are you going to hold him to the fire? Or work together and be productive? Using honey will produce better results.
I agree, the pattern does not indicate racking.
On the side, people like to rag on and deride IKO but when this happens to IKO around here they pay for it.
Good luck with GAF they are going to try to weasel out of this.