these...alternates you speak of... :-p
In Empire, the alternates are all released in some form, but not all of them were digitally remastered and included on the SE set.
For Jedi, the alternates are said to be missing.
For A New Hope, there is some debate about the origin of the alternate take of the end credits, but there were some 400 takes so variations in orchestration do occur and are slowly changed during the recording process... happens all the time.
The alternates are things like an Ewok Insert to replace a portion of "The Forest Battle," or "End Credits" from Empire which is really just a different editing of the tracks (there is the album edit and the film edit. The Album is more 'listenable' where as the film Is more accurate to what was wanted I suppose but is more jarring.)
There is the alternate "Han Solo in Carbonite" cue which is on the set but is hidden. There is the alternate "Finale" which isn't on the set and is only on the anthology. There is the alternate Sail Barge Assault which came from the masters for the Anthology, not from the actual masters so the quality isn't as good as it could be. On top of that, it's the "Album concert suite" recording session, not the actual film recording.
Example of differences between Film and Album concert suite recording:
"The Ewok Battle" and "Ewok Battle Concert Suite" ... they are almost literally the same, but there are slight orchestration differences and the concert suite is longer of course. But if we only had the concert suite, we'd still would be missing a great cue of the film version of "The Ewok Battle."
These are things composed for the films, usually at different points or for different edits of the film. When the film is re-edited, Williams would come in and rescore them such as Sail Barge Assault which is said to have been one of the most complex edits of the original trilogy becuase of there being so much action going on simultaneously. Because of this, the edit went through several versions. Williams scored the original edit.
Then Ben Burtt went back and kept tweaking the scene and adding in more, extending some portions and shrinking others. Then Williams came back in and rescored that edit.
Burtt, however, kept working until they "got it right" as Lucas said, but by then, Williams was no longer available to re-score the scene and record the music so they had to use what they had and edit it to how you hear it in the film.