All ethics of the deletion aside, matching on metadata is a weird, crappy approach (and that itself is pretty consistent with my other experiences with iTunes).
It shouldn't be hard to imagine that metadata will have collisions, and include something like a hash of the actual data.
I don't know if it's intentional filling in for songs they couldn't license or metadata matching gone wrong, but occasionally on Spotify a song on an old album is replaced with an inferior remix from a newer album.
Intentionally or not, history (what songs actually were on an album) gets edited unless you manage music files yourself.
(The Apple behavior described in the article is way worse than what Spotify does, of course.)
It shouldn't be hard to imagine that metadata will have collisions, and include something like a hash of the actual data.