in theory if you wanted to you could use hardlinks to retain the original file structure while also having a nicely organized version available. most of the Arrs support this although TBH I do not trust them with the files I wish to preserve in this way. Since there’s not too many of them I just zip up copies of anything I want to retain exactly and let the software work with a duplicate. And hardlinks of course would still be subject to editing like retagging.

Of course if you are accustomed to your library being organized in this manner and it suits you, then there is no reason to change. :)