I've gone back and forth with the author via email about a few points related to this email, and per his request, I'm sharing them here:

1) The common MOD to bVII seems to be a byproduct of Trey/Mike treating the major and mixolydian modes as interchangeable. When the band is in a major-key 'rock' jam (basically anything that isn't Reba/Wingsuit lydian bliss or phrygian/middle-eastern stuff like Taste/Limb By Limb/Light), the ^7 and ^b7 are usually treated as equal. I suspect this is why moving from A to G in DWD is such a common occurrence. I also offer as proof of Trey/Mike treating major/mixolydian as equal the start of the jam in Slave: Mike almost always ignores the G major chord, playing around A, A, D, E, instead of Page/Trey's A, G, D, E progression.

2) Why do you think the band so frequently goes from i to III, but rarely I to vi? It seems like the only way they move to minor keys is through mode mixture (I to i) or an abrupt move which is ill-prepared (i.e. Trey just starts playing a D minor chord because he wants to play some song in D minor next!). I can't think of many jams where the band makes the MOD vi shift, but I can think of one famous time it was attempted by Mike: http://phish.in/1997-08-10/harry-hood?t=9m30s (Mike slightly modifies the Harry Hood jam: every second time through the D > A > G progression, he plays Bm > A > G). It sounds amazing, but I can't think of any other times off the top of my head that this has happened. Why might the band avoid MOD vi? It seems to me (as a bassist), that moving there would be quite easy, and I have no doubt that it's as easy as MOD III. Just a curious observation.

3) Since most MODs come from Mike and Trey, do you think they consider the playability of the new key for Page? As you know on guitar, moving from one key to another is kind of a cakewalk if you're not using open strings, but for keyboard players, moving too far too quick could be a pain. Perhaps this is why most MODs are relative major/minor, or one step away on the circle of 5ths? (MOD IV or V). I'd hate to be Page when the band is jamming in Eb, and then goes MOD bVII into Db major. "Thanks guys... this is great." *immediately moves to ambient washes on CS60/Rhodes* (Actually, I just looked up the Page gear video to get the name of the CS60, and stumbled across this exact quote: https://www.youtube.com/watch?v=1EyKV1wRvT8&feature=youtu.be&t=4m08s )

4) Finally, I suspect the reason that 555 hasn't taken off as a jam vehicle for the band is the awkwardness of that closing progression: Bbm > A. It doesn't fit any traditional key or mode, so it seems like Trey has a tricky time finding a real melody to put over it. He tends to rely on one bar phrases, then a bend over the tricky change, eliding the transition. It's almost like that song needs to do what Split Open and Melt does rhythmically. SOAM starts with that extra bar of 9/8 every fourth time through, but eventually the band abandons the rhythmic intricacy for an open jam, eventually returning to the original rhythm to signal the end of the jam. (I know it wasn't always like this back in the 90s, but since 2.0, that's basically been how it goes). 555 could do the same: Bbm > A for a while, then settle on one of those chords, and go deep. (The way Simple eventually settles on either F or Bb.) The problem seems to be that the Bbm > A progression doesn't leave enough melodic options open for the band to settle into a space where they can move into another jam in just Bbm. It goes around the progression for 2-3 minutes, then Trey realizes he's out of options, and hard segues into Light or something.