I do not understand it well yet either.
I think fastboot mode is different from USB/HID mode. I downloaded a Windows command-line tool from freescale that lets me push code from host PC into kindle RAM when it is in USB/HID mode, and execute that code. Their example shows using uboot.bin.
fastboot is more for flashing new firmware without needed signed update packages.
AFAIK.
yifanlu is welcome to correct me here.