5.0.x were incremental updates with using of binary pathces. 5.1.0 contained whole new files and just copied them into place. Could you note the pattern? There wasn't 5.2.0 update (just like there wasn't 5.0.0 update). And 5.3.0 just pushing the idea to the extreme and copying whole new filesystem and kernel images over the old ones.
Maybe it was just easier to distribute whole rootfs instead of specific patches/files?
But, BTW, expect whole new Kindle going OTA right to you with 5.4.0.