imbue? you mean elemental? regular with or without elemental are both regular attacks, not skills. What you described about add temper is correct, it used to apply (maybe still does haven't tested it) to elemental damage. It still doesn't mean it makes your regular attack a ''skill''. Elemental damage can be reduced with elemental resist, you get from psy/int and from rings or accesorys.
The fact that SD armour works in the new maps/dungeons is because the mobs do not have auto attacks, every hit they do on you is actually a ''skill'' their auto attacks are skills, thus SD armour reduces the damage. This is exceptional tho and you won't see it back in other parts of rohan.