Initially, I didn't really understand the reasoning either. If there was a player that they valued higher than Yorke, then they should have gone with the other player.
That said, as with most things, it comes down to money. I guess the Sox feel like they have a very good chance of signing Yorke below slot money, thereby freeing up some extra money for their 3rd rounder. Are the Sox better off being able to sign what would typically be a 2nd rounder and their 3rd rounder, or would they be better off signing a 1st rounder but not a 3rd rounder?
I guess with the uncertainty of prospects, the more you are able to sign, the better off you are. We do still need to replenish the farm.