i think the reason they say not to mix silkies with standards is because some of them have a skull that is not entirely enclosed, so a peck on the head could kill them. i think even with an enclosed skull, a standard chicken could do serious damage to a silkie or any other small breed bird. But if they have grown up together and are getting along, then that's a different story.
i would think introducing another bird of any kind would cause some friction and pecking, that's just normal. At least a japanese would be able to fly up and away from any aggression. i personally keep my big girls separate from my little girls.