@ixtab: Sort of: The 128K you find usable is internal to the SoC.
The i.ROM code burned into the SoC only deals with things that are present on the SoC.
(With a slight bending of that rule if using external USB device instead of the on-chip one.)
I think (not actually confirmed by myself) that the i.ROM code has enabled the SPI controller, so that you have the choice of reading the SPI rom from the DRAM to get the DRAM setup specifics.
If you haven't yet read AN3996.pdf, you will probably find that a better starting point than the U-Boot source. At least after reading AN3996.pdf you will recognize the CSF defines when you stumble across them (where ever they may be - I don't know).
Brain Fart: Since the Java bytecode engine is in hardware, you might be able to do this all in Java at the "client" (Kindle) end of the communications link. Just don't forget to service the watchdog.
Note: The K3Flasher is also a cross-platform application based on libusb - -
It might be a better starting point than the application that is being discussed here.
At least the original author is available at this site.