The custom u-boot images I built, which are included in the MfgTool profiles, are the first-stage u-boot that fits in OCRAM, with the addition of a single line of code that temporarily sets the bootmode to one of (main, diags, fastboot).
When you use the fastboot version, it initializes SDRAM, and then loads the larger u-boot bist (Built-In Self-Test) from mmc into SDRAM. The kindle fastboot protocol resides in u-boot bist. With an erased mmc, it cannot load and cannot support fastboot mode.
It would be possible to create a (more complex) MfgTool profile that can also load u-boot bist over USB.
But with existing tools, the easiest method may be to flash mmc (including u-boot bist) over serial.
One problem is that the portion of /dev/mmcblk0 that contains u-boot and u-boot bist appears to be all zeros when you make a backup copy of the first 32MB. It may be necessary to export a backup of the mmc using the serial port...
Does anybody know how to get a backup image of u-boot bist from the mmc on a K4 or K5?