A while back I was asking about the cap on the column wheel. One of the purists mentioned that it is the requirement of the Geneva Seal... I think he is right.
According to the latest PP magazine (Volume II Number 6), in the article that introduces the 5959P, it said "the two column wheeels that control the chronograph hands stand proud as well. As required by the Geneva Seal and Patek Philippe traditions, they are capped by polished and chamfered crowns."