If you look carefully in the top left corner of one of the screenshots, you can see that a Pokemon Crystal game pak is being used! Sure, the Japanese letters for "Bashaamo", "Massaguma" and "Taneboo" are there, but it could just be a list of the Pokemon that are stored in the Gamecube, and not Pokemon Crystal.
This, my friends, seems to be the way to get the unobtainables.
What about the "!" and "?" Unown that weren't available in GSC? Well, they'll probably be obtained by maybe sending over the A-Z Unown to R/S, or something like that.
Anyways, Pokemon fans, I bet Pokemon Box won't just be about storing the R/S Pokemon, only!