That's been one of the two biggest flaws in this game for as long as I can remember throughout its development. The progression flags are not clear, and the dev's requirements to unlock the next part of the game seem arbitrary. Often times when I played it, it seemed like there was a lot to grind, or I'd feel stuck after trying a bunch of different things, but then something happens for no apparent reason and the story snowballs itself. I don't fully understand it either.
The other big flaw of this game was building it in RPGM. The VN style of the game is always 100% better in Ren'Py, whether someone likes Ren'Py or not.