That may well be the case in the future. We have an upcoming overhaul to the site which is currently not compatible with games which branch off with different versions/chapters. The current method of hiding everything behind spoilers isn't sustainable as it becomes harder and harder for new users to understand that mess. If we can figure out a method of cleanly integrating chapters with the upcoming update I have no problem with merging the threads; until then they're staying separate.
All you need to do with that is just to say in the OP which order to go in, if people can't read that is their own fault. Making multiple threads isn't going to help new users understand anything, they just have to download stuff from multiple threads instead of it being in one thread.
Its the same problem, if anything it makes it worse. People might not know they need to play the previous or future stuff if all the threads are separate, they may not even know it exists. They see the "Completed" tag and think the game is complete, not just the first chapter.
"How to play"
1- Download and play Chapter 1
2- Download and play Chapter 2
etc.
I don't think it can get any similar than that. You can add a FAQ's section in the OP too.
Sam you quoted my post as I was editing this, just to be sure you saw this new bit since its not in your quote. Its not thread based, and you don't need a bunch of spoilers.
I don't know if this is possible, but you could probably add new sections at the top of the thread ( where the reviews and discussion buttons are) that contain the different download links, everything is still in the same thread but the links are all separated.
"Discussion" "Reviews" "Chapter 2 Links" "Chapter 3 Links" etc.
Everything is separate but still contained in one thread, when you click them it takes you to a new "OP" that contains their respective links.