that makes sense, especially if you been working on it for some long lol. Since it's already there it definitely makes it equivalent to dealing with spaghetti code. You just dive in here and there to get what you get.
As for the organization, it's not impossible. It's definitely a bit hard to do, but again I will reference the easiest and earliest example that I used the walk-through for. When I was curious if something would happen if I let the dark mage girl finish her unlucky charm, I had to jump way down the list of quests. Yet her follow up quests are up above it as if you could possibly do them first. Which... you can't. Because you still have to get the key to unlock the door and meet her for the first time. There were other quests that were very obviously just out of place in the quest list, which is what makes me think it's either alphabetical or numerical. But if it's entirely random, that's even worse xD even if you made a wide open sandbox that players can do and go as they please, there is still going to be some order to progression of quests and where the player should be given their items and levels etc. You already said the explore and find out what areas are to strong or not was intended, and I'm fine with that because I plan to do similar things. But when even the walk-through is spaghetti... I will also bring up how I know the walk-through has lil quick jump links, but they don't seem to work on mobile. So I tend to do the "find in page" option to find specific words I hope are in the thing I was looking for lol. That's why I said it's tough for the creator (you) or whoever would put together the walk-through because you would have to know the ins and outs of the game and think which segment would come first. Even when it's a wide open sandbox, these games do still have hooks and flags that need triggering :P