Moral systems in and of themselves, completely flawed in concept. First and foremost is the misplaced idea that either a good person should get rewarded for being 'good', and a evil person should be rewarded for being 'evil'. In reality, what you get rewarded on is based on the opinions of the people around you, and some people would argue that God, or their deity also plays a role in this. So Pillars of Eternity has this part right. It makes sense that there is no 'good' and there is no 'evil', in the case of a fantasy setting. I believe, myself there is an ultimate moral in real life, but in a video game setting this is thrown out the window since my religion (or most religions on Earth) are in PoE.
A good person should never inherently be 'better' than a bad person, and vice versa. Some good people have good fortune, some don't. Same with evil people. This is why any sort of dogma that good is better or bad is better, or either gets better gear or rewards, is silly and futile in the conveyance of a real narrative. Unless gods come into play, which changes the game completely. Although normally the idea of 'good' is displayed by the god that you choose, but in PoE, I believe they have implied that gods are selfish and do things for their own benifit. This being the case, an ultimate morality is definitely out of the window.