The problem with any streaming service is having a live recording matched by non-live version, if that's the only one available. You can get by that, but no one wants to change meta data for millions of "incorrectly matched songs"
not to mention the time it would take to go through manually, since "smart playlists" don't exactly do what Apple says it does. which is a huge downside.
Apple Music may have its problems, but I dare to say that replacing live recordings with studio ones isn't one of them (anymore). I have a LOT of live recordings and none of them was replaced with the studio version. At some point, if I recall correctly, Apple changed the matching algorithm to a more accurate sound fingerprint one, so this shouldn't happen. It's a different thing with remastered versions or whatever, though, in which case both songs sound exactly the same, but are "only" mastered differently.