I think the main point that is being overlooked is that this is Kiper's board; not a consensus of what is found most everywhere on the Internet or in print.
Think about it logically; aside from the top couple of prospects (Johnson, Thomas, Adams...), how many NFL team's boards are going to stack up the same come draft day. Look at the Bills last season; did anyone else have Donte Whitner rated as a top eight prospect, or higher? Maybe, maybe not. The simple fact is that every NFL team, and probably Mel Kiper, know more that 99% of the wannabee draftniks (myself included).
Aside from casual observation of college games, surfing the Internet for data, and performance test result like the combine and pro days, what more does the average person know about these players?
Scouts and people like Kiper do this as their living. They live and breathe pro prospects. They get to see these players firsthand, interview them, and spend hours and hours breaking down their game tapes.
I give them a lot of credit and if someone like Mel Kiper has Ted Ginn ranked as his 10th best prospect, but doesn't have Alan Branch on his board, I believe he has a good reason for it, and isn't just throwing darts.
Of course, wrong decisions will be made (look at all of the NFL draft busts), but overall, these guys really know what they are doing.