So I noticed that the augmented fire/frost/shock perks do not work for runes and cloak spells, and furthermore dual-casting them has no benefit (but still consumes 2.5x magicka). This may be true for expert and master level spells as well, I just haven't gotten there yet.
I would imagine this is a bug, but perhaps this was intended for some reason? Thoughts? Can anyone confirm if any other destruction spells are not using perks?