I had the misfortune of playing a cleric of Eothas in PoE and it really became a detriment to my enjoying both stories considering how integral Eothas is to the setting, and in the second game. The story kind of encourages you to have a certain view of the gods that I had been earnestly roleplaying against (unwittingly), but without really giving the options to you to come around to it gradually, like what happens in your Magran companion's story.
I recently replayed Deadfire again because I never played the ending with the added content, it still didn't quite hack it. It felt like anything, like the endings to the move
A.I. or Bioshock Infinite, the story became so ungrounded that it kind of implodes into itself.
Josh Sawyer has some good talks about Pillars and Deadfire where I think he cops to a lot of the shortcomings in the story. The biggest thing I remember were the points he made about how the factions in Deadfire are very interesting, but aren't really tied to the main story, meaning that interest in the world can run counter to the narrative's impetus. Of course, considering how the game ends, maybe they were trying to make a point about temporal concerns.
This is the one I remember
at around 26:30 he gets into the post-mortem Nevermind that, I was just scrubbing through it and it's all pretty much post-mortem