indeed, i'd say every song on Alive in Athens is overdubbed to hell. the two setlists culled to make it are both on setlist.fm and it shows very little overlap, as mentioned, and even the overlapped songs weren't played the same (i.e. "Dark Saga" -> "Last Laugh" was only played that way in one of the gigs) and i think most of the songs weren't played to a click (except maybe "Dante's Inferno") so there wouldn't be consistent timing across the different performances of those same songs to use as, for instance, the second rhythm guitar. thus, i'm quite sure Jon re-did at least one side of the rhythm guitars, if not all of them, on the entire thing. most of the solos and transitions to/from clean guitar also sound too perfect to be from the original tapes.
the difference between Athens and this upcoming release, obviously, is that Athens wasn't overdone. Jim Morris knew how to mix all the ingredients to keep the live feel and mix the crowd without sounding like it was a studio record layering in a fake crowd, like those classic Metallica songs from Kill 'Em All that were re-recorded for Jump in the Fire and had fake audience sounds plastered in between. (i'm sure the Athens crowd is quite enhanced, though!)