So...I also posted this issue over at TDP, and user Trowski suggested a workaround that does the trick:
Enter an AFMA for an older lens (one without the serial number on the chip, like the 70-200 II), then power off the camera. Turn it back on, and the AFMA menu should show zero and the serial number will be zeroed out (though if you take a photo I'm willing to bet it will still show the adjustment you made). Now without powering off the camera, remove the lens and put it back on (or at least turn it enough so the contacts aren't touching). Go back into the AFMA menu. I'm willing to bet you'll see your adjustment value and the serial number.
Trowski is a genius! It's kludgy, but it's a workaround. After doing so, it seems to persist for one power cycle, too. After doing that with my 70-200 II, I put on my 40/2.8, and it showed the previously set -2 straight off. Power cycling then zeroed it out again, but just loosening and remounting the lens with the power on brought the correct -2 back. Also, changing the AFMA then doing the workaround results in the new AFMA being applied, and restored after a repeat of the workaround, as long as you change the AFMA setting right after the lens unmount/remount, when the previous setting is visible. The new setting also shows up in the EXIF, regardless of whether or not it appears zeroed out on the menu.
Some (including Bryan at TDP) have reported this issue, others say they don't have the problem. Personally, I always power off the camera before changing lenses - I wonder...if I routinely changed lenses with the camera powered on, would I not have noticed the issue? As stated above, the value seems to be saved, and recorded in the EXIF, just not displayed on-camera until it's forced to re-recognize the lens.
Sort of a pain, but it'll do until a firmware update comes along...
Thanks again, Trowski!