Something I didn't pick up on before was that Jamie mentioned about distances when shooting over someone.
My idea (without any detailed knowledge of the rules in question

My rules are originally written for Late Roman civil wars - late C4th & C5th.
It makes sense as you are not firing at something you can see if you are behind another unit, like "Golden Shot" you're relying on directions given by someone else.
My thoughts were that the target for a plunging shot is smaller & better protected than that of a flatter trajectory eg a shield held overhead can cover all the head & body.
Yeah my thoughts were based on the idea of "indirect fire" rather than plunging fire in general.