I've obviously made some progress with Binding of Isaac Rebirth mods on the 3DS and have managed to get The Binding of Undertale to work.

Ensure 'Game Patching' is enabled in Luma's configuration Hold 'Select' while powering on your N3DS

Extract 'luma' folder to the root of your microSD Recompiling as a CIA actually saves 58MB as it replaces some of the original music Launch 'HackingToolkit3DS' and enter 'cr' to recompile the CIA, choose the name, enter '3' for minor version and '0' for micro version (if you don't enter the version, it will always ask you to update and fail) Extract the 'resources' folder from 'luma/titles/titleID/romfs/' within the zip and place it in 'ExtractedRomFS' (Overwrite everything) You should now have 'ExtractedRomFS' folder and a bunch of other files Launch 'HackingToolkit3DS' and extract the contents of the CIA (ce for CIA extract, you don't need to decompress the code.bin) Take your decrypted Binding of Isaac Rebirth CIA and put it in the same folder as PackHack

The modding of isaac undertale