Interesting ideas, we'll think about it.
Regarding the 1 nodes- you're not the first person to point that out.
My thought initially was that I like these places in the puzzles not being empty.
As you pointed out, the puzzles also reflect the narrative and the in-game character's mind, so I felt that the ability to make it one filled node instead of a whole mattered.
That makes sense. I wonder if having some additional feedback would help make them feel integrated. Something like You get a "clarity" score based on how many times you have to redraw each path, or something like that. And so in the puzzles that reflect moments of certainty in the story these kind of nodes could be more common reflecting the character's understanding of the situation. Meh, even I'm not sure that's a good idea.
