OK, I decided to throw caution to the wind...
Ultimately the update worked, but not without one rather scary hiccup. First time through, connected through the 500X, it failed with the familiar MIDI error message, which I've seen before with other updates. However, this one was also accompanied by the entire alt. tuning knob lighting up royal blue. Multiple attempts would not clear the error, so I unplugged and powered off everything.
Oddly enough, when I reconnected to Monkey, the JTV registered as having 2.1 installed, despite the fact that it never finished the update. Also, I had elected not to keep the JTV models I had on the guitar, but when I connected to Workbench after the failed attempt, the models I had previously created were still on there, so the process obviously hadn't completed.
Attempt number 2 after powering everything off worked as advertised, and connecting to Workbench through the 500X works fine. So what went on the first time, I have no idea...I remain very puzzled as to why flashing firmware is still so hit or miss...but I've had that repeatedly that since the beginning, so it's certainly not peculiar to 2.1.
I still find, as have some others, that the Strat models need string volume adjustment...the low E, A, and D strings jump up and smack you in the face, especially in positions 4 and 5. But this is easily fixable, and also not a new issue for me. I suspect that string gauge may contribute to this...I play 11's....so perhaps the increased tension on the piezos is the culprit...just guessing. At the end of the day I don't care though...that's what Workbench is there for.
Popping sound when switching patches seems to have gone bye-bye...or at least significantly diminished, although I have not really experimented with it much yet. Still futzing with string volumes right now.
All in all, it seems to be a big improvement, so I gotta give credit where credit is due. All except for the update process itself, which frankly sucks, and is still relentlessly annoying. Of all the flipping back and forth with firmware that I've done, it's more or less 50/50. It has failed on me multiple times (both thru the 500X and with the goofy USB dongle), but never with the entire alt. tuning knob turning a different color...no idea what that means, if anything.
So at the moment it's working...and I'm not gonna poke at it anymore unless something craps out....probably won't go near it again until the next update. Still way to buggy a process...batting .500 will get you to Yankee Stadium, but it's not an impressive stat for a firmware install.