I don’t see the problem with the atom, especially since I’m not in the business of giving out songs.
I'm not in any such business either, but I just don't appreciate it when a company that I pay money to adds secret tracking codes into a file without telling me beforehand.
It's no big issue to me personally, as I don't get into MP3's much to begin with. CD's and vinyl usually sound noticeably better on my system, and so all of this is rather an academic point for me.
If you enjoy iTunes and don't mind what Apple has done, then more power to you and full steam ahead. :-)