Let's say I find a piece of armor that gives +X% to my physical armor. I don't see a "base physical armor" in my arcane stats, so off of what character attribute is this percentage being applied? Is it off my base value or off my base value + the armor value of the piece itself?
%modifiers are applied on top of your total physical armor calculated after adding up all the physical armor equips you have equipped. Basically %Armor modifiers stack and end up modifying your total base armor.
It does not apply only to the armor piece or only to your base value.
In your arcane stats you will only see the final value and the %modifier in effect for that type of armor.
Base value though not displayed can be calculated off of it if you want to verify this.
If you really wanted to check this, you can verify it by removing all your armor and adding the equip in question to see how it affects these values.
Hope this answers your question.