Theres nothing different about his history. He was still engineered by halsey, he was still human but at the point where the librarian "does something" to hime that is the point where he is no longer and organic being but a digital being in the same way as the knights. ... just a more successful transfer where he retained all his consciousness unlike the knights of the didac. And why would the composr turn her to flesh and blood when he apparently spent his whole life attempt ing to turn organic life into digital life not the other way around.