Maybe this has already been tried, but...
Has anyone considered the possibility that Square could have left (either accidentally or on purpose) "secret" entrances on the overworld map? Remember that the entrances aren't always obvious--i.e. Vortex Pt. It would be time-consuming to check, and probably a complete waste of time, but...it's always possible that some out-of-the-way tree, or some position behind a mountain, or some other weird place on one of the maps, COULD contain a link to a secret location.
For that matter, such links would be possible as well from within the dungeons/buildings/areas we all know of.
As I said, probably a waste of time--especially considering how much ROM checking has been done--but I'd be interested to know if anyone's ever actually scoured the maps for such a thing.