Rincewind: On the iPods the bootloader is completely safe to mess with. In their cases there's a hardware bootloader (which Rockbox doesn't mess with) that loads a software bootloader from the disk's firmware partition (which is what we replace) that then goes on to load Rockbox.
So if someone screws up the software bootloader, they can still tell the hardware bootloader to take them into disk mode. But you do NOT need to compile the bootloader with this patch. This patch only applies to the regular build, and while it breaks bootloader builds the bootloader binary available, or the fact that you're using the iPL Loader, means that fact doesn't matter.
As well, a version of the patch that doesn't break the bootloader build is now up.