The point is that the story is very tightly wound so that all the different kinds of problems many different people (including yourself) have in the world, the chickens come home to roost in the final actor as you understand the similarity binding them together. That similarity, of course, is foreshadowed throughout the entire game in the scriptures of Wael you find throughout the world: what is an answer without a question? What does struggle mean - your struggle against Thaos, all of 'humanity' (& other races)' struggle against their own lives and disasters like the Legacy, Thaos' struggle against the 'false gods' - what do they mean when you understand that nobody can guarantee an answer for you?
When Thaos asks you at the end, why would you want a world without the gods? You can give a number of answers. This isn't just flavour text. Through it, he (the game) is asking: what did your journey and your struggle mean, and that of Eder for his brother, Sagani for Persoq, etc., mean? Can you find meaning when the game does not throw you a Nice Happy Ending, and can characters find meaning in a world without gods?
This is why I thought Iovara's relationship with you is also revealed appropriately. On its own it's not a particularly powerful conceit - here's this woman you've never met and she just had some investment in your decision in a rather lackadaiscal way - but the fact that you understand the Apostate, just like the Grand Inquisitor, is also searching for an answer - an answer which, after hundreds of years, you can never find. The fact that you can only give the Apostate some rather stupid reasons ('I didn't like you') or choose to keep silent was another nice touch. It would be thematically inconsistent to give her 'closure' by just visiting her and saying a couple of things after all those years.
The one weak point is the Gods revelation can be pretty jarring, "oh hey wat" after what is a very religious world and a religious story. I like that they tried, though - and Durance's story is important here, too, the fact that Magran cannot 'see' him. I would have preferred an ending where Durance ends up broken, though, and not a happier 'I'm ma own man' Durance. I wonder if this was one of the things changed from MCA's 'darker' original drafts. But then, we also get that with Dak'kon.