Many interesting points here - it'll be a while before I can give this another close listen, but there are a few other things to consider:
You ask who else would play that repeated 8-note riff through Dark Star? I believe the Dead wanted that riff there - notice that Garcia himself keeps playing that riff for the keyboardist until they get it right. That sounds like a definite "play this riff" instruction to me, and would hardly be necessary for Pigpen who'd already been playing it for months. (TC also played that riff, at least initially, and only in the intro.) My impression now is that the keyboards sound as little like Pigpen as they do like TC. It just does not seem like his style to me, and not just because of the tentativeness. But I'll have to listen again to point out examples. Pigpen had been playing Stephen since at least late May/early June (and the Eleven since January), so it doesn't seem likely he'd be so tentative here. (Check out his playing on the early Stephens to compare.) I had always taken for granted that it was Pigpen or TC, without really listening closely - but the idea of an unknown third keyboardist opens up much more exciting possibilities for this rehearsal. It definitely seems to me like they're teaching the keyboardist the material - and since Dark Star/Stephen/Eleven was a huge chunk of their material, it's something a new member would have to learn. The other thing is, when would the Dead be in a studio recording a rehearsal? Unfortunately we don't know much about their studio time in the summer of 68. We do have one studio jam-session from August 13, and part of another from September 21, at the Pacific Recording studio in San Mateo. This was right at the time when the Dead were getting really unhappy with Weir & Pigpen, and the Sept 21 session has Garcia & Lesh playing w/o Pigpen and with an unknown third guitarist. Gans suggests it may be an audition for David Nelson - "Nelson recently told me the story of trying out for the band at Pacific Recording. They made him play The Eleven and The Seven." By the start of October they'd started recording songs for Aoxomoxoa. I don't know if Pigpen even appeared in the studio for the album sessions - it makes sense that, from the start, they might have wanted a different keyboardist, at least for the studio recordings. (Just like they later brought in keyboard guests for American Beauty.) So that seems like the most likely timeframe for me. Trying to get Stephen/Eleven just right for album recording would also explain why they're taking such trouble to go over & over the parts - initially the full medley was to be on the album. (Notice they don't bother as much with Dark Star, which was never a candidate for Aoxomoxoa.) Granted, if this is a September session, then there's the question of why they're having so much trouble with the Eleven when they could knock it out flawlessly at the live shows. (An uncertain keyboardist may help explain that.) Someone may have to closely compare this Eleven with the other Elevens from summer '68...which won't be easy! Another clue, as noted earlier, is the Sputnik section of Dark Star. This simply doesn't appear in any of the Dark Stars before the end of August. If this studio rehearsal was from mid-summer, you'd have to wonder why the Sputnik section wasn't played in the Aug 21-24 shows. It appears in almost all the Dead's Dark Stars for the rest of the year - and my guess is, comparing this section with the other versions will help settle the right date for this recording, since the Sputnik jam developed considerably from month to month in '68.
