By faking some header info I suppose?
To me this means they definitely have a way to transfer data between systems. They did say they weren't going to release it, and quite possibly the sheer magnitude of the hack has guaranteed it.
E: To clarify, they have a way to modify the download titles. Once you reach this level it's pretty much guaranteed they actually have the keys to decrypt the digital games (unique to each console) and change things in them like the region.
Now, say if two people had their keys and the files. In theory that means they have a way to share games between systems. These two aren't interested in unlocking Pandora's box with piracy and something like this might make them reconsider a public release, if one was planned at all. Hell, after they are done, they could let Nintendo know the hack they used so it is unable to be used further.