Protection from Energy effects process first currently when it comes to taking elemental damage.
An example of this is to run through the purple worm stomach in Belly with 40+ acid resist. Your Acid protection will quickly deplete even though once depleted, your acid resistance will completely mitigate the acid damage.
If protection from elements was processed after resistance and absorption, then it would be a lot more useful of an effect. It would harmonize with resistance and absorption and be bonus hitpoints against that specific element.
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For a bonus on top of that, make Stoneskin more useful for characters that have some other form of DR. If you have DR 1/- and Stoneskin, the Stoneskin still depletes 10 a hit instead of having the 1 blocked by regular DR and 9 blocked by 10/adamantine.