I mentioned this to Hasu, and he thinks that the reason that the "Boot" command in Soarer's code doesn't work is because it is written specifically for the Teensy bootloader, and basically the "boot" command tells the board to jump to a the bootloader address which is a bit different on these chips. Should be fairly easy thing to fix in Soarer's code, but we'd need an update to Soarer's code to do that. I've offered to commission that feature, but like many others, haven't heard back from him recently. Assuming that feature were to be added, then they would be upgradeable from then on.
Other thing Hasu mentioned was that it might be possible to interface with the bootloader itself to get it to do a reset through Arduinio programming software, and if that were possible, then they would all be upgradable. I don't have any Arduino programming experience or know what to try though to see if this is a possibility.