To be honest, he plays best in a back 3 but the back 3 Pirlo plays is really a back 4 in the defensive phase and the timing of Danilo's movements to the right back position can leave him exposed and therefore makes Bonucci look worse than he is. Bonucci's distribution and long balls is what makes him unique and why coach's like him.
Also I have a feeling that Pirlo really wants a McKennie style midfielder also helping a lot in defense. Perhaps Arthur's positioning needs to be refined in the system too.