The existentialist aspect is most certainly prevalent. Too prevalent. It ruined the story for me, in combination with other factors. When I finished the first side-character story (Kana), I though to myself: "let me guess, all of these long and ambitious quests by these dudes will reveal nothing at all because the writer had a thing about existentialist". Bingo. The story should not have been that predictable.
@Verenti: you mentioned animancy linked to existentialism. It is much more linked to Hare Krishna and Spiritism. Animancy proves that it is not an individual's will that shapes reality. But it is an outer force that affects his soul in relation to how he lived his previous life.
There is a pseudo science vs. religion discussion that does not make sense at all, because the gods actually have godly powers in the game. And animancy, which is supposed to be the science side, actually proves the supernatural.
It feels as though there is a pervasive real-world influence of an atheism vs. religion debate influence in the game, which is is, quite frankly, a disappointment, because it is just the fad of the current times to praise atheism. Good stories are timeless. Think Planescape: Torment. That game was a better example of what you were saying about power and reality.