Regarding alternate takes, check the scenes when THX visit SEN, almost all scenes Donald Pleasence did are lifted from other takes and digitally manipulated into the scenes, whenever there's a shot of the two actors in frame, his eyeline doesn't even match Duvalls', he's looking and talking in another direction, looks terrible. Those few scenes that are still left from the original in that scene is often digitally reframed, zoomed, shifted sideways or whatever, similar to what was done on Star Wars.
Even the lighting/cinematography on some original scenes have been tinkered with, actors faces that was earlier in shadows are suddenly in light etc. There's much more changes to this film than what most people realize, albeit subtle.