The longbow is not the piercing weapon, the arrow is and the example (in brackets) clearly shows this.
I believe this is where we disagree, I'd say something that fires a missile is the weapon, and the missile is just that. The missile.
I wouldn't consider a 7.62-bullet a weapon, but an AK47 I would. Same goes for bows and arrows. The size of the weapon is H, it imposes a -40% penalty.
When you start making all kinds of situational modifiers for this type of thing, where do you stop? OK, I'm shot with a longbow at long range, surely the velocity of the missile is now decreased, lessening it's impact, which should reduce the penalty for being impaled. At close range (or closer) by using modifiers, the penalty would be increased. It is a game, not an exercise in mathematics. When people try to over rationalise or try for too much realism, IMO, it creates layers of complexity that are simply not needed.
I agree, luckily just taking the Size of the weapon solves this, so a short bow is L, a longbow is H and an arbalest is E. That corresponds to a -30% ; -40% and a -50% penalty.
Either way, the argument that using impale as a valuable debuff on range still stands, even just a -10% cumulative penalty is pretty useful.