Sharpstick, I tried to make this simple earlier but you seem to have missed the point. The design or inefficiency of the crossbow doen't affect the kenetic energy or trajectory at all. It all comes down to arrow speed and arrow weight. Yes it requires much more draw weight to get an arrow going the same speed as a compound bow but once the arrow is in the air it doesn't matter how it was launched. You seem to be missing a big piece of the puzzle. Yes the arrow length will play a role as will size of fletching but it's minor in comparison to weight and speed. Let me put it simply. Shoot the same arrow at the same speed out of a compound bow and and a crossbow and the trajectory and energy will be identical.

Also, larger fletching like that found on many vertical bow arrows will slow their speed more rapidly than an arrow with smaller fletching.