How does having nicely organized files, independent of an application used, have anything to do with making playlists, adding files, etc.? All that you mention is in the application domain, and is not hindered by good organization of files. Turn off iTunes' automatic reorganizing feature, and all that stuff you talk about works fine, with neatly organized folders and files. Any work done by iTunes' database is entirely abstracted from the files themselves. That was not the default last time I gave it the chance, but it's a mere checkbox.
How does it help other applications to not have good files organization? How does that help Audacious? Slimserver? VLC? Random file manager of choice (Dolphin)? New stuff on a new OS that isn't out yet? It doesn't. Do I care about getting to a random new file from everywhere? No. It's going to be in a big messy pile, until I decide to sit down and sift through them all.
There is no staring at folders going on. It's a matter of accessibility, done from experience of doing it poorly.
Files in folders properly named for what is in them is the best way to organize files for easy access from any application and platform. It in no way gets in the way of doing anything with them that depends on the application's features, nor managing them in other ways at the same time, even with iTunes.
