http://ipodlinux.org/Firmware is a good overview of the Apple firmware's organisation and the ipod boot process.
As you will see, the main Apple firmware image (the OSOS image) on disk has a useful header, which includes an "entry offset".
The Rockbox (and IPL) bootloaders work by appending themselves to the end of the OSOS image (meaning the Apple bootloader loads it from disk to RAM with the main Apple firmware) and then simply adjusting the "entry offset" from the usual value of 0, to point to the entry point for the bootloader.
The "shuffling" that ipodpatcher does is to move all the subsequent images (AUPD, RSRC, HIBE) to make the space to extend the OSOS image with the bootloader. The OSOS image itself doesn't move.