I haven't finished the whole game yet (just finished chapter 2) so I didn't read all the posts in detail to avoid spoilers. I also think that, so far, there are some unexplainable inconsistencies in "the big picture" of the absolute. But I just wanted to propose that a completely coherent story would only be possible in a "visual novella" style game without important choices. So any choices you make are really fake and the story will proceed over 1 linear path from beginning to end.
The more branches and alternative paths that you create on the way, the more difficult it will be to avoid plotholes or inconsistencies.
Personally I'm willing to live with those storyholes to be able to walk different paths. Now of course, I 'm in my first PT, if it turns out that the different paths are illusionary and don't change much in reality (like eating lots of tadpoles and embracing the dream image, vs. rejecting her and all tadpoles) then that would be rather disappointing.
I would disagree with this lightly, in the sense that I agree with you that by giving players control of the narrative, it makes it very likely that holes will be introduced into said narrative, but I think that's a question of narrative consistency. Narrative coherence - in my mind at least - is a different thing that's very much achievable. When I say that the narrative is incoherent, I mean that it's various different parts don't work together and results in a story that really doesn't make a lot of sense at several points. Plot holes are one thing, and I think those are acceptable if it means a better story. But the story should still have internal cohesion and those holes should not be present consistently throughout the game.