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.
