I still fail to see why it is so important HOW iTunes organizes the files.

To me the important thing is that iTunes knows where the files are and can find them when I want it to. Where the files are, and the structure they are organized by, is immaterial. iTunes can do all the work.

Doc

I keep additional files in the same folder as the music (cover scans, etc). I don't always use iTunes - sometime I need to find a track by navigating the file system. Sometimes I play music on my Linux box, or share the music to my Xbox. At some point in the future, I might want to use a different media player than iTunes. For all these reasons and more, it's important to me to manually organize my music.