Yes, PER applies even to short jump shots. I believe that there was a note to an update that suggested that you should think of LP as inside scoring and PER as outside scoring, but everything in between is determined by a blend of both. ATH, SPD, IQ & BH make a difference as well.
For your example, +2 is not necessary. I would look at other ratings too. If that guy had no ATH or REB and was poor at FTs, then sure, but otherwise +1 or 0 would be fine. On the other hand, if that guy had high ATH, good at the line, and your opponent was likely to attempt to defend the perimeter, then +2 is giving away too much. The key is to watch offensive efficiency. If he seems to be hitting 3's at the same % as 2's (or at least 38%), then let him jack them up, but not otherwise.