The problem is that "with a handicap" is in itself ambiguous. People sometimes use it positively, sometimes negatively. That is, you say that Shin had a two-stone handicap, that can in itself be understood as either "Shin was given an advantage of two stones over the AI" (the reality) or "Shin was playing with a disadvantage, giving the AI two extra stones" (the more common reading of "to have a handicap").