Imo, Pedigree has nothing to do with it. Take 2 chocobos, lets say P1 and P9 both trained with grade 1 food, that race against each other in the R-100 class. the P1 will probably be around Rank 35 and the P8 maybe Rank 10. Their base stats gonna be about the same, because else they couldnt race in the same class. The stat gain from food is much higher for the P9, but he trained 10 times, the P1 trained 35 times, so there wont be any difference.
The difference comes from using grade 2 or 3 food, which most people wont do until they reach their perfect chocobo. So they could fix this by lowering the prices for better food.