Yes it does have a special protocol that is completely retarded. Winamp uses the same protocol. When I first connected my device as mass storage device, I went to browse the music folder and I couldn't believe my eyes. I don't know why would they complicate things in the organizing of folders. It was a total mess. I will give you an example.
I had an album with various artists copied using Winamp, I found that it was scattered in folders each having the name of the artist, then inside this folder a folder with the name of the album and then inside a file with the name of the song. I mean what are ID3tags for?
I decided to test, so I copied another album with various artists but I just copied pasted the ONE folder that had all the songs. To my surprise, I could browse the album using genre, artist, album and song title.