The question you pose has a very simple answer: The 2nd and subsequent shots you have on the Par 4 and 5's are dependent upon the 1st shot (tee shot). In math/stats, we call this a dependent variable- it depends upon the prior. Now granted, on the Par 3's the 2nd and subsequent shots are also dependent upon the tee shot, but you have a perfectly teed and level lie with the shot into the green with the Par 3. On the Par 4 and 5's, since the iron (2nd) shot is dependent upon the tee shot, you might be in the rough, behind a tree, awkward lie, etc. which is producing a bigger variance in your score. In other words, there are other variables to consider with the Par 4 and 5's.
A stat that you would want to look at is the average distance of the Par 3's vs. the average distance into the greens of the fairways you hit. Of the 6 fairways you hit, what was the average distance into those greens? Of the 4 greens you hit, how many were Par 3's? What was the average distance of the Par 3's?
If the average distance of your Par 3's were say 105 yards and the average distance into the greens of the 6 fairways you hit were say 150 yards, then there's your answer. As with all stats, the answers are there, you just have to interpret them the correct way. And, vice versa, it is very easy to mis-interpret stats...
I hope this helps!!??