I just read some interesting answers to a similar question at the ffshrine:

Set 3 uses quite the same material than the two other sets. Its interest though is to bring alltogether 1) all the original album mixes "remastered" from the old original CD, and 2) All the new remixes, *ie* sessions (Anthology) improved with LP for both missing orchestration (like percussions and flutes that sounded too far, almost unexistant on the sessions) and higher sound range that reach the original album's one. It's not just a simple edit btw, as it seems a lot of people often believe because they're too busy to read or to listen, but a total remixing thanks to tremendous sources synchronization job and pitch correction, all checked on both the session and film mixes (Belbucus version, if that means anything around here).

The Anthology session mixes lack range a bit, and are a bit more shiny sound-wise. So the 3rd set offers even more consistance than the 2 other ones, even though they do it rather well... Wich is pretty cool alternative if you don't always play in a stroke the two CDs of a complete score.

But the original LPs are heavily edited and the 3rd set here gives the complete cues, with two exceptions due to the length of a CD - or the unavailability of a 1980 album version for those edited out parts... ?... Pick one. So, here's the big difference anyway: it's called "The Original Album Reconstructed and Completed" because it uses and contains all the original album material, in a way or another. It doesn't reproduces John Williams's album arrangement.