Any feature that moves your files around automatically is going to do something that you perceive as wrong or damaging eventually. Starting with a blank organized folder and letting Roon import into the folder via drag-drop is good. We do not recommend pointing Roon’s organized folder feature at your existing music library–Roon will undoubtedly make at least a few changes that you don’t like, and it’s difficult to reverse those changes once they’ve happened…
We have been discussing how to make the feature less dangerous. We released with it because it’s required in order to support drag-drop imports, and that requires file renaming machinery. IMO the feature isn’t really finished as a whole.
My guess is, we’ll reformat the feature so that shuffling files around is a bit more manual (making it way less scary), and probably merge the watched and organized folder features into one concept. But we aren’t quite there yet.
For now I’d stick to the watched folder for everything but drag-drop imports.