I had a minor flashback when I read that.
Years ago when I decided to give iTunes a try (big mistake), I made the mistake of leaving the "Keep iTunes Media folder organized" option checked. iTunes almost completely re-organized my lovingly organized CD rips. The most egregious action was to move thousands of files into a "compilations" folder.
For example, John Lee Hooker's album "The Healer" was broken up into 8-9 different folders. iTunes thought that since Bonnie Raitt, Los Lobos, Robert Cray, Canned Heat and others were guest artists that they needed their own artist folders inside the compilations folder. I don't want to know how many hours I spent re-ripping my collection. Never again.
I don't care that iTunes is finally being broken up into 2-3 other programs. Apple won't have the opportunity to screw up my collection up again. Rant over.