Moe also played the 4 and at times the 5 for St. John's last year because they only had 6 scholarship players. He played out of position and was unable to focus on his outside shooting. Rumor is his draft stock keeps rising because scouts are pleasantly surprised with his shooting.
The notion that a guy played out of position in college is overexaggerated. The worst example this year is saying that Beal played out of position at small forward for most of the year. I don't know what even playing like a small forward means but when Beal got the ball and he got it as regularly as the two other "guards," he played his normal game.
In a similar vein, Harkless may have technically been the PF his freshman season but he wasn't a back to the basket type, hunkered inside the paint. He played like a wing most of the time and initiated his offense from outside in. He was as much as SF as a PF.
Also, why would Harkless playing the 4 or even 5 affect his shooting? Plenty of 4s and 5s stroke it at a high rate. If anything, his shooting should have in theory benefited from going up against slower guys who couldn't challenge his shot as well as quicker wings would have.
It affects him because the Red Storm wanted Harkless attacking the basket, so the reps in practice, were primarly, as you accurately mentioned, him getting the ball in the high post, facing up his man, and driving, etc. With D'Angelo Harrison hitting tons of outside shots, and the Red Storm having a dearth of big men, they needed Moe to bang down low. No priority was placed on him playing behind the 3 point line because then there would be no chance for offensive rebounds, etc. Your point is well taken that it's not like he never practiced his 3, most likely, but to not understand how it greatly affected what he was doing in practice and what types of shots he was taking in general, is shortsighted.