First, I mostly agree with beberlei on his suggestions. However, you may be designing yourself into a trap. Your domain appears to be considering the title to be the natural key for a track, which is likely the case for 99% of the scenarios you come across. However, what if Battery on Master of the Puppets is a different version (different length, live, acoustic, remix, remastered, etc) than the version on The Metallica Collection.
Depending on how you want to handle (or ignore) that case, you could either go beberlei's suggested route, or just go with your proposed extra logic in Album::getTracklist(). Personally, I think the extra logic is justified to keep your API clean, but both have their merit.
If you do wish to accommodate my use case, you could have Tracks contain a self referencing OneToMany to other Tracks, possibly $similarTracks. In this case, there would be two entities for the track Battery, one for The Metallica Collection and one for Master of the Puppets. Then each similar Track entity would contain a reference to each other. Also, that would get rid of the current AlbumTrackReference class and eliminate your current "issue". I do agree that it is just moving the complexity to a different point, but it is able to handle a usecase it wasn't previously able to.