And this right here is why I don't particularly like ad hoc DM assigned bonuses.
I think there are other bonuses and penalties in the game system that don't make sense in some scenarios where a DM assigned bonus or penalty would make more sense.
For example, when attacking a prone foe, the attacker is at -2. At range in a 2D more or less level situation, this makes sense. He's presenting a smaller profile far away, so he's harder to hit.
But when the same foe is prone in a 20 foot pit and the archer is shooting down at him, he should be easier to hit than if he was on his feet and could more easily dodge an attack, not harder. Looking and shooting down into a pit is merely a 90 degree turn from shooting horizontal. Why is shooting horizontal at a vertical foe (i.e. not prone) a 0 penalty, but shooting vertical at a horizontal foe (i.e. prone) a -2 penalty?
This is a case where game simplicity trumps logic. But I would have no problem if a DM made some adjustment to the normal rules to handle special cases like these.