The difference, in my opinion, is a scouts ability to differentiate between "what are they missing that can be taught" and "what are they missing that can't be taught".
Ie. DK Metcalf. In a re-draft he's a top 10 pick, but he fell because he "can't run anything but a go route". The ability to see that he's got all the raw tools that can't be taught, combined with route running, which can be taught, will result in a freak of a #1 WR.
Also, I think some scouts, though they won't admit it, have a "big school" bias and can't accurately scout a really good player on a really bad team.