I don't get the big deal, honestly. From a real development standpoint, I believe all files compiled into the same folder is the best route. You can use the virtual folders in the Xcode environment for grouping and organizational purposes while coding, but not having to worry about the correct path is a GOD SEND... I love that I just have to reference the name of the file and not have to remember where it is "located" in sub folders. Virtual Folders with a single root folder is the best development environment. It is not like you ever have to SEE all of the files in the same folder, that is only when compiled or when pathing and Xcode takes care of that for you. In the dev environment, you can see all the virtual folders you want, so unless you are naming your files the same name in different folders, which is not the best development practice in any situation, I do not see where your problem lies. You are not having to see all of these hundreds of html files.
Some people here are new to development and this is their first step into writing web or standalone applications, so they haven't had the hours of frustration with a bug in their code that ended up being a pathing issue... if a coders problem isn't a missing semicolon, coma or unmatched open/close objects, it ends up being a pathing issue... From a developers stand point, not having to EVER worry about pathing is the best... I have been a developer/coder for over 20 years, so from a newbie standpoint who simply looks at it in the same way they browser around their computer, I can understand their frustration as well, but after they have been coding for any period of time, they will realize what an awesome feeling it is not to keep checking what folders your files are located in.
I don't see it as a flaw but as a feature!