I saw this on Baseball America website and it seems relevant here. I think this is a good summary of the importance of speed and the importance of knowing how to run, and how scouts account for the difference. The "thumb on the scale" comment is in reference to how a scout might adjust the raw grade upward or downward to account for these other factors that influence on-field performance.
"Traditionally, players’ speed grade is based on either his home to first time or his 60-yard dash time. That is a concrete time to base a grade around, but it doesn’t really allow much leeway to account for instincts, understanding of how to get a lead, reading pitchers and base stealing ability. Since it’s a tool grade and not a skill grade, there is some logic to that point, but base running experts say that it’s harder to teach those skills than one might believe. Again, the write up and possibly a thumb on the scale has to account for the differences between a speedster with no clue of how to steal a bag and a slower runner but one with impeccable abilities on the base paths."