The only reasonable explanation is that Game Freak designed Greninja that way.
My 2 cents? It's because Greninja is the fastest of all 3 starters. At base 115, it's tied with Starmie and faster than Infernape, so if you Spec'd/ Band'd Greninja, it will deal some pretty massive damage while being able to outspeed its threats and a lot of common Pokemon.
Delphox is relatively slow competitively, considering it's base 100 speed which is outsped by threats like Zoroark and Mienshao, and Chesnaught is tied with Breloom at base 70.
Soo my reasoning for Greninja being base 520 instead of 530 is because it would be slightly OP'd if it had that speed and base, idk, 100 atk or 95 sp. atk, considering that it does learn Extrasensory and Nasty Plot via level up, so it has something to deal with Chesnaught.