If both systems modded just make both use the same movable.sed and you have a portable sdcard.I can understand where they are coming from. I'm just also thinking about the possibilities of things that can be done with 3DS/CCIs which cannot be done with CIAs. Such as usage on other consoles without the need of having to extract the saves and transfer them over to another console. I'm thinking more of easier portability and it being as easy as ejecting the flash card and/or SD card out and putting it into another 3DS system without the hassle of having to extract the save and inject it into the other system.
Any other benefits?