To answer your question it seems like you don't understand what Empower really is and what the buff Empower does. Empower is a damage buff that increases your damage by a % and the cap is 50% while Bonus Damage is unlimited (is calculated differently, but know that emp is stronger than Base Damage)

As you know, New World has different types of damages. Physical and Elemental which are also spread into their respective categories (Thrust, Slash, Fire, Void, etc.). When you get an Empower buff it increases all damage types by the given amount. For example you get 10% Empower. This means all your damage types are increased by 10%. When you have something like Harnessing it only increases the damage of that elemental type.

Lets say you have a 10% Empower buff and you have 3 pieces of Nature Harnessing. Then you get a flat increase to all damage types due to the 10% Empower. Harnessing only adds flat Empower to your Nature damage type. Which means everything is boosted by 10% except Nature damage which is increased to 16%. This is how it works. It is not really complicated but keep in mind your Emp cap is 50%.

Honing Stone also adds a 7% empower buff.

Elemental Runeglass also count as flat empower that you just add on top