So, it seems that save data for Fates is universal, as in, any save works on all versions provided you have the content needed.
Take my Japanese SE for example, used svdt to extract the saves from the cartridge, used svdt to inject it into my NA Birthright Cartridge, works like a charm.
My friend has Conquest (NA) with Birthright DLC purchased, copied my save onto his game and it also worked.
So not only is the romfs file structures for the games the exact same across all versions, most of the files are also the exact same, the only differences so far seem to be the translated text files (obviously) and very few changed mechanics such as the Face rubbing/skinship, every other file is an exact match with the same structure and everything as I had pointer
here.