Just because the arrow has a weaker dynamic spine [the longer arrow] does not necessarily make it less accurate.
Consider that on a given length, a greater FoC [based on center of mass] gives more effect to the fletching, then take two shafts of the same build only one is an inch longer... While the calculated FoC is slightly lower as a precentage, it is actually slightly farther from the center of length and therefore slightly farther from the fletch giving the lever arm between the fletch and the center of mass greater effect. If the bow tune was absolutely perfect and the fletch didn't have to correct flight it's not an issue, but if the tune isn't perfect and the fletch has to correct flight, the longer shaft will when all else is equal correct more quickly.
Regardless of tune however, a robot [or shooting machine] will put the same arrow into the same hole regardless of bow tune, and while the holes may be in different locations this isn't a measure of accuracy as you could sight into either shaft and the other would be the "less accurate" arrow; i.e. in the above example if the machine were sighted using the longer shaft, the shorter/stiffer reacting arrow would appear to be the less accurate one.