Nick, this is NOT true on a RPi3 that uses external storage.
I took the unmodified (no /boot/boot/overlay file) system, made the one line, lirc change to kodilauncher.sh from earlier today, ran recalbox-save-overlay.sh. The system now boots, but does not start emulationstation. The system displays the batocera splash screen, it dims and then instead of the emulationstation carousel, it displays the batocera splash screen with the version/timestamp text. The system is up - I can ssh into it, but emulationstation does not start.
If I unplug my external usb hard drive, the system now starts and the kodilauncher.sh fix is there.
The recalbox-save-overlay.sh script does not work with external storage. Is there a workaround?