[ He rubs it, because the phasing had felt weird and he had enough nightmares over death and his spirit that making sure he really was corporeal suddenly took precedence. ]
Most likely a mix of the two, depending on who they were. The events are discussed in history, but I suspect a lot of what the governments of Earth know is classified, including the technology and practices used to make the Augmented Humans. That sort of thing has been largely outlawed, in my era.
[ He had understood Khan's anger - not in that he shared the experience, but he could understand why he would hate humans so very much. He would hate someone too who had kidnapped him and altered him so completely without his consent. And then to try and use him as a weapon? Strip his humanity?
It was no wonder they had turned on humanity and tried to destroy them. It didn't make what happened right, none of it, but he couldn't exactly fault Khan's motivations either. ]