If you're still interested (it's been, what, four months?) I had modified the IR-GTS script to invoke the save function before it sends. I used it a bit, but the integrity of the Pokemon made with IR-GTS (And especially the little edit I made, for whatever reason) seems questionable, so I stopped. The name and hold item seems corrupted most times, amongst other things that occasionally get flipped. I would definitely check it with PokeGen/Check/whatever. But you could try it if you'd like. Just replace sendpkm.py in IR-GTS\src with the attached file and delete the corresponding .pyc file
It only saves if it's a .3gpkm.
EDIT: False alarm. There were some Pal Park trash bytes in some places, so I read it a bit wrong, but it seems every Pokemon has nearly the exact same data as before it was transferred. (Nearly, meaning IR-GTS treats every .3gpkm as it was from Emerald, regardless of its actual origin, amongst other lazy things)
sendpkm..zip