I always saw runes as a very equal thing. A rune adds x amount of damage regardless of what it's on. It's a magical kind of thing, that when added to a weapon, gives it an effect depending on the skill of the tinker.
Another way to see it, should armour that is bigger offer more protection when they get armour runes added? Should armour with higher innate AC offer more AC when it's runed? (Maybe it already does, I don't know).
