The patcher doesn't account for CTR NAND.
One way to check if Luma is running from CTR NAND, is to see if "boot.firm" doesn't exist on the SD card.
That's Luma's fault for only loading files from the boot source, and not from SD. Maybe an option to "allow loading from SD" in CTRNAND mode would be useful, but checking the code, I don't think it would be easily done without a rework on how the filesystem code works. Perhaps double-checking if it doesn't exist on CTRNAND then try on SD, but that sounds like hassle.