When the institute created Synthetic humans they created them as learning robots to preform tasks beyond their programming functions, this can be seen when you talk to the leader of synth recovery and retention when you ask him about courser training, they take the most suitable synths and train them for combat and to kill or shut down rogue synths. this ability to learn has manifested itself in other, unexpected ways as well. Diana a rogue synth working for the Railroad learned to help free other synths as well and how to fight against the institute in the process. Brotherhood Paladin Dance another rogue synth learned to fight for the brotherhood and super mutants because he believed he was a pure human and that synths and super mutants were abominations against nature, bigotry is a very human response. Father believes that synthetic humans are servile robots and nothing more but if that is what he wanted to create he should have programmed them to not be learning robots because somewhere along the way they will learn that humans treat each other with respect and not simply as a servant cleaning up after them and they will learn right from wrong as well as the synth programmed to act as your son shows when he is afraid of being taken away from Father and the institute, it is likely that even if you offered him the same exact training regimen and schooling he would receive at the institute he would still wish not to leave because in actuality he loved father and knew it was wrong for you to take him away.