To lay it down very simply.
Most natural armor bonuses are designed to give you just that, a bonus. An amulet of natural armor gives you +3 natural armor. However, natural armor bonuses do not stack with other natural armor bonuses. So for example, the tarrasque has a huge natural armor bonus, that wouldn't stack with that amulet of natural armor.
The spell barkskin is worded differently. The reason is the designers want you to be able to use the spell when you already have natural armor. So you cast barkskin on the tarraque, and it would get the bonus.
Most natural armor bonuses are designed to give you just that, a bonus. An amulet of natural armor gives you +3 natural armor. However, natural armor bonuses do not stack with other natural armor bonuses. So for example, the tarrasque has a huge natural armor bonus, that wouldn't stack with that amulet of natural armor.
The spell barkskin is worded differently. The reason is the designers want you to be able to use the spell when you already have natural armor. So you cast barkskin on the tarraque, and it would get the bonus.