Yorke is still high in their rankings due to proximity to MLB. He's still on the younger side being a HS draftee. His defense is better than initially projected. They have noted specific concerns in regards to Yorke, but it's not like the guys right behind him are wart-free (Perales, Abreu, Wikelman). Cespedes could leapfrog this grouping, but it's too hasty to do that for a guy who hasn't played stateside yet.
IMO, the Sox system is pretty deep, but there are no top end prospects aside from the big three (Anthony, Mayer, Teel). Everyone else is pretty far behind that group. There are some interesting guys for sure, but being interesting isn't the same as being a top 50 prospect.