OK, getting back to this after a real long time
I guess the reasons why I think it's G#+ are because a) it sounds like there is a very clear walk up from C to Am, with the G#+ working perfectly as a passing chord, b) I don't hear the counterpuntal walkdown of (c) > (b) > (a) that would be present within each respective chord if you were to play C, E7, Am in that passage, and c) the 3 of G# (C) doesn't sound off over that chord. If it were an E7, that C should sound off as you play along. The last point is a pretty minor point, though, because E7 sounds OK, and by the reasoning of the third point, it should sound off to some extent if the band is playing G#+ there.
So, imo, either they are playing G#+ or they are leaving out a note (C in the case of G#+ or B in the case of E7), thus leaving it ambiguous (which certainly isn't beyond them
In the end, retaining the C and E notes on the G and B strings, respectively, as you move from C through G#+ to A just sounds the most like what's happening on Reckoning.
Also, like Phil, Weir is definitely prone to and quite capable of using substitutions and bizarre voicings. If Phil plays a G# as a passing tone there, it frees Weir up to play either a C *or* a B in the corresponding passing *chord* as he pleases. That kind of harmonic ambiguity is why they were able to keep so many jams so interesting.