On the ATK side-track: I've gotten a bit further (but only on the knowledge side, nothing practical). The thing is, ATK is basically a) a memory patcher, which is used in the first step to set a few SoC registers (memory mapped) to certain values in order to set up RAM type and timing etc.; b) it is an image uploader which then pushes a custom boot loader onto the device, and c) a frontend for some functionality of that boot loader.
"Download" is probably from the view of the device, i.e. it's a firmware uploader. I didn't dare to play with it yet. "Dump" should dump to a file; however, I did not manage to get it to work. I carefully sniffed the USB connection, and it seems that it uses almost the same protocol as the serial bootloader (which I recognized when I saw this:
http://api.ning.com/files/6TZuB9Rylm...ad_Protocol.py). I couldn't make something out of the "06 06" command that is used in USB downloader mode. But it should be possible to write an ATK clone for linux, for example.
However, I don't think the Kindle SoC is correctly set up by the default scripts that come with ATK. That would need careful investigation of the u-boot initial device set up, I think.