What I never understood about the Order's religion including the story of creation is who created the people?
This is my guess and reasoning behind it otherwise it makes no sense to me! What about you guys and gals?
I think this is apparent in many creation myths that don't completely play into the creatio ex nihilo idea that everything was created by one almighty God alone. This is most apparent in many non-monotheistic religions, as that not one source is the origin of all. In many indigenous North American myths there existed "people" before the advent of the world as it is now. The creation myth in SH3 describes the beginning as "In the beginning, people had nothing.", which is similar to how many Native American religions (South and North) saw the beginning in a form of primordial chaos.
Going by what is given from SH2 onward, it is not unlikely to assume that a lot of the creation myth is an amalgamation of Native and Christian beliefs which mixed during the time of the settlers. SH2 also implied that there was a first phase of settlement which came before the current people, so it's quite likely that the indigenous religion had already been affected by Christianity at the point when the later founders of the Order came around.
It is also said about man that "They fought endlessly, but death never came. They despaired, stuck in the eternal quagmire.", which implied a form of quasi-immortality. So these "people" were not exactly the form of humans as they live today, but rather an origin race from which current humanity descended.
Then follows the scene of Birth through sacrifice "A man offered a serpent to the sun and prayed for salvation.", so the sun was clearly deified, but the myth does not clearly define it as a god.
Again if we assume that Christianity and indigenous beliefs mixed in this religious construct, then any god higher than God had to be crossed out of the origin myth.
This is comparable to how Amaterasu Ookami became considered the highest god in existence, and the personification of the sun in Japanese myths, when the emperors bloodline was connected to her in the restoration period. The creation myths of Japan mention many legendary periods before her, but many of them were more or less ignored when religion was streamlined.
Remnants of a former creation myth can be found in the presence of fellow gods, portrayed as Gods creation and/or transformed into the Christian concept of angels. Those would be Lobsel Vith and Xuchilbara, as well as the presence of Valtiel as Gods midwife.
Thinking about it, if the Order is ever featured again in a game in one way or the other, I'd find it interesting to find more apocrypha and forbidden tomes about their beliefs, portraying more of the conflicting myths behind their religion.