There's a good argument for not putting track ratings into the music files: They're subjective, not objective data.
i.e. If the music file is shared by multiple people, they will not all agree on how much they like it. They'll all agree on things like the artist name, track name and publishing date though. (Well, within reason.
Sometimes people disagree on what to put in those fields as well.)
(People may also want to rate files on read-only network drives or optical media, I suppose.)
As usual, I'd say the ideal would be an option about where to store the rating data. 
(Personally, "nowhere" is a good answer as I've never seen the point of rating files. If something is garbage, delete it, and everything else is so dependent on mood that the rating doesn't mean much to me. Could be because I'm an "album guy" rather than a "shuffle play guy", though.)