Might be out of line when I say this but maybe not too wise to raise a necro thread? But then again, you might get roasted for using a new thread, *sigh*.
Back on topic, yeah, you could probably export your desired pkm using one of the many programs out there and then use PkHex to place the same Pokemon into your box in a later X/Y or AlphaS or OmegaR save.
Edit: I'm going to cut out my explanation for the Nand setups and backups and just say this...that setup seems unnecessary, if you happen to already know about PkHex, why is your setup more appealing if I may ask? Can you even have 2 3ds's signed in on the same account, feel like there would be a huge risk in doing that? Why use another 3ds to system transfer the same account when theoretically you could backup your SysNand and restore that nand to the emunand and then they both have the same account...not sure that works that way and if that is a plausible solution either...Assuming you know, not trying to be rude.