The only pieces of gear that are outside the natural damage cap is Burtgang(Mythic Sword) and Aegis(Relic Shield).
And gear like twilight torque, defending ring, Mekira Meikogai, that german named belt, the mollusca mantle, askar feet and ogier's helm all have straightforward -DMG taken. This applies to physical, magical, and breath damage.
The Mythic sword adds more PDT outside the natural cap since it is a Mythic, and the Aegis adds more MDT outside of the cap since it is a relic(but these are recent-ish changes).