It looks like the offset of the instruction that needs to be patched is known in advance, so there's no need to open it in a GUI editor (for example, to do some searching for the right place). A python script would suffice -- just open the file in binary mode, seek to the correct offset, and write out the new instruction.
Thanks, these are great suggestions. The project is young and currently we are prioritizing adding support for UI, SEP and interrupts. We do accept code contributions so please contact if you would like to add support for something like this.