I saw this coming somewhere around the first paragraph. Those students who are trying to transcribe lectures and not actually learning anything? My guess is it's because they're burning cycles mentally saying "'the', I need to find 't' and an 'h', aaaaaand 'e'. 'quick', where the hell is 'q'?"
As a parallel, take Jimmy Page (Led Zeppelin) as a guitar player. Sure, his playing was sloppy as hell when playing live. But the man knew the fret board. He knew all of the places any note could be played, he knew which boxes will allow the riff he wants to play (in fact, I doubt he thought "which box?" but rather "here's where I need to be"), the man was comfortable with his tool and the guitar has the appearance of being an extension of his hand when he plays. He never looks like he's mentally saying "okay, I need an A# next, which is...". This allows him to move on from rote mechanics to making incredible music.
Typing is the same IMO. If you struggle with typing, the first thing you're likely to do is reach for the mouse for anything other than text entry. Which means you reeaach over to the mouse, then mooooove the mouse, click, and...what was it you were doing again? Then when text entry time comes it comes out as "M...y...C...l...a...s...s... ...*...f...o...o". The tool is taking up mental cycles when it should be more of an extension of your thoughts.
It's been argued on HN and elsewhere that typing speed has little bearing on productivity for programming since one spends more time thinking than typing. My counter to that is that the two probably intersect more often than you think they do, and when they do you don't want to be burning cycles figuring out which finger to use to reach the "w" key.