Its most likely locked to the position rather than ninja for instances where you are missing a ninja would force you to reapply chakra anyways. Equipment only gets automatically applied since there a finite amount and the game just puts them on chars essentially randomly. With chakra orbs youll have excess orbs so instead of the devs taking it upon themselves to decide what orbs they want on new ninjas, they associate your "chosen" chakra to a position to avoid this.
A pro to this would be if chakra orbs actually worked as one would expect (dmg reduction, *ions, a cpl others def dont work as you would think). The values are part of a calculation that give you a percent which we arent privy too, games like WoW would give you the %'s to allow you specific customization of stats.