>a computer doesn't know the difference between formal and informal this seems to indicate that Alpha isn't truly above Fan Hui in strength. Also the formal games were played with fast game rules,

I'm not sure if I'm misunderstanding you, or you're misunderstanding the situation, but the informal games had faster time controls than the formal ones: the formal games had one hour of main time, while the informal games just had byo-yomi (3 periods of 30s: if you take more than 30 seconds for a move, you "use up" a period).