As far as I know the issue arises from the fact that before even getting a pip boy you can use the spav/vats.
However I think I read around that the 3rd generation synths were produced only after (many years after) that Shaun is kidnapped. Also the main character has a son, so in my opinion there is no way that it is a synth. The only thing is that it was replaced at some point, maybe the real character died during the war but as I said above, it doesn't seem to me that 200 years before there were already apparently human synths, maybe there weren't even the 2nd generation ones yet.