Is there any difference in the data of a Pokemon you transferred legitimately through the Transfer Lab for Gen 4->5, compared to just dragging the Pokemon between the two save files in PKHeX?
My end goal is a fully self-caught living dex that will eventually get stored in the Pokemon Bank, so I want to be sure nothing ever "taints" my Pokemon files that could cause an issue long down the road. I do have the ability to copy my save file onto a DS cartridge and do a legitimate Transfer Lab move, but doing that mini game for a couple hundred Pokemon is something I'd rather avoid.