Say you hit 10000 and armor reduces that by 30% to 7000.
If the mastery gives you 20% (I'll go with 20, could be 15, 25, who knows) of that as Holy. It will get it's value from 10000 because that's what YOUR damage range.
Armor just makes it lower when you actually hit.
So of that 10k you get 2k converted as Holy Damage (8k physical 2k holy) if that's the case then the only portion of the strike affected by armor's 30% reduction would be the 8k physical.
In the end the strike would turn to do 7600 damage instead of 7000.
It's very likely that's the way it will work, but for now it's just speculation.