It took me 8 years to realize that the sole survivor, the main character of Fallout 4, is actually a synth. For example, the leader of Acadia asks you an unusual question. In this case, The protagonist can't remember anything except the day the nuclear war started. And judging by other synths, memory problems are precisely characteristic of them. With this in mind, it's more likely that the main character isn't Shaun's real father, but rather another experiment orchestrated by the Institute's leader. He likely replaced his deceased father with a synth and then staged the protagonist's unfreezing.
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