Atheists generally believe that all religions are man-made and manufactured in a very obvious fashion. The allegory here is not subtle. The religious establishment that Thaos represents is 1) a system of lies created for the purpose of control and domination, 2) relies on the premise that people are too weak-minded to bear the truth, 3) obscurantist to the extreme and hostile to "science", 4) entirely willing to commit atrocities in order to preserve the status quo, and 5) not only unnessecary for the world's peace and prosperity, but an active impediment thereto. These are the same arguments and criticisms pitted against real world religion by atheist polemists. Add the fact that Thaos' organisation has many similarities to the Spanish Inquisition, and that Thaos himself is the ultimate religious boogeyman, and the ending feels like a preachy progressive morality play wherein an atheist protagonist is beating the stuffing out of a strawman that wears a papal mitre.
It is within Obsidian's creative freedom to make whatever points it wants, but personally I found the ending's heavy-handed allegory to be a swing and a miss. Despite the early association of Thaos with Woedica, it wasn't clear throughout most of the game that the narrative was building to a smash-the-church climax. Iovara is too under-defined and introduced too late in the narrative for me to care about her person or her valiant undying stand against the establishment, and it doesn't help that much of her dialogue feels like it jumped straight out of an argumentative youtube comment (the "my reality is true whether you believe it or not" or somesuch line caused an involuntary eye-roll).
The big revelation was a surprising twist, sure, in that I certainly didn't predict it, but it wasn't an effective one. The motivation behind the engwithan manufacture of their counterfeit gods falls flat for me; a civilization that was (with the exception of its skill at animancy) less advanced than modern Eoran civilization proved the nonexistance of god(s) with such certainty that it altered the course of their civilization and the world... so we're dealing with a civilization that learned how to prove a negative (a logical impossibility) before it mastered metallargy, or chemistry, or invented the printing press. Not particularly convincing. But, okay, I can put up with dodgy logic. The larger issue for me here is that this twist about the truth of this setting was delivered in the very same game that first introduced us to it. I've only just started learning about these gods, I'm not yet remotely invested in them, and therefore I'm not emotionally affected when they are discredited by a sudden revelation that comes with all the theatrical power of sitting on a half-inflated whoopie-cushion. If Obsidian had made Baldur's Gate 3 and written an ending which revelaed Ao the Overfather as some super computer responsible for generating the multiverse, or as the eventual apotheosis of a time-travelling Tiax or something, I might have been impacted. As it is, exposing these gods as fake really meant nothing to me in the context of the narrative. It only becomes meaningful if I consider that Obsidian is not just imparting information about the gods of their new setting, but rather is making a statement about religion in general. Which again is their point to make if they want. I just find it dissapointing to get to the end of the road and find nothing waiting for me but one-sided allegory.
I have to agree here. The ending made me sit back and stare at the screen thinking "What the hell did I just play?". I had been enjoying the game up until the end...now, I find I have little interest in replaying it. Incidentally, releasing a message like that just before Easter probably made the impact a bit worse.