In case people are interested, here are Mike (the author)'s responses to the four points I brought up:

1) Totally agree. The major/mixo and minor/dorian are pretty much the standard pitch collections. You rarely hear any of them playing the natural ^7 or the flat ^6, right?

Much the same way there is no major II chord (it's a secondary dominant of V, or V/V) in rock music, the flat-VII chord is really just a secondary subdominant (IV/IV). I suspect its origin, which seems to have arrived with the rise of guitar-based rock music in the 1960s, has to do with the properties of writing music on the guitar itself, unlike writing on the piano, etc. That's a huge study for some to take on...

2) I wondered about that. I don't know of any jams that modulate in the opposite direction (I-vi). I really wonder why and have no clue. That's an interesting one you point out; I'm reminded also of Reba jams (a sort of never-ending IV-V progression, or E-flat to F, in some phantom B-flat key that isn't really there): sometimes Mike will go to G minor (vi in B-flat) and hang out there for a long time. It's worth exploring, though, if you've got the juice (do it!).

3) LOL. I wonder! Though I doubt they give it much consideration... I'll have to listen back to the Randall's Chalk Dust, which goes all over the place (including, I believe, to D-flat at the end...).

4) You may be right about that. I remember at the debut of 555, when they got to the jam, listening to Trey struggle to improvise over that B-flat to A progression; lately, though, he's abandoned that in favor of just playing in B-flat dorian/minor etc. Which is what he should do, in a sense, since that A is sort of just an altered dominant of B-flat (in an obscure kind of way). I can't imagine it's holding them back, since you're right: a la Melt, they could just ignore that alternation of chords and just go somewhere from B-flat. I think we'll see that eventually.

Also, in a subsequent email, we discovered a pair of MOD vi in the Dick's 2012 Light, at 6:50 and 15:37-16:10 (depending on where you want to drop the needle!) Interesting that this famous jam includes TWO of these rare modulations (rare for Phish, not for music), and yet the band seems reluctant to revisit. (Not a single MOD vi in 2015).