Turns out you can symlink ext4 -> fat32 but not the other way round.
I created a new modipy.conf in /boot and deleted the original in /etc/modipy.
Then: sudo ln -s /boot/modipy.conf /etc/modipy/modipy.conf
Now I can edit the file on the SD card from a windows machine - just don't use notepad! It needs to be an editor that understands Unix line endings.