If Atmel ever did fix it, maybe bossac could begin by detecting the bootloader version?
The idea of uploading an optimized bootloader to RAM is actually pretty crafty. If someone ever did go to all that trouble and added it all to a new version of bossac, wouldn't you consider accepting the contribution? Of course, I think the odds of anyone ever going to all that trouble are pretty slim. But maybe someone could convince Atmel to release their bootloader helper code under an open source license, so someone could use it as a starting point?
But really, I just obsess too much about data transfer speeds and protocols. I should probably stop now and get back to more urgent work.....