I agree, the story elements are so disconnected from the game at large. The life and story you see in the cutscenes (even then it can be a bit hard to follow) ends when the cutscene does. All the lore that's built up doesn't seem to apply during normal gameplay. As you mentioned, for the forest being so sacred and the constant threat of upsetting the wood, we seem to be able to quite freely run through it and do whatever we please. Kill anything, do anything.
The same goes too for the apparent beastmen threat. Unless the beastmen are a secret society they're the most non-existent immediate threat I've ever seen. The world's danger isn't very apparent and the lore is so... "other," that it doesn't feel like it's even really part of the game.