I have not encountered any that do, but there's no reason it couldn't be done. Several of the programs I use at the office are Java-based, but they're not the kinds of things you're likely to see on an end-user's desktop.
Do you know what programming language they use? By that, I mean the programs that mod FF7 and the programming language of the game itself.
Another question is, how did the New Threat & Hardcore mods modify the battles on the world map? Also, the New Threat mod was originally going to add a forest to the world map. This suggests that changing the world map is possible. In that case, it should be possible to bring back certain places such as the Temple of the Ancients and Mideel starting the Disc 3 portion of the game. It should be possible to add new places too, such as the Lifestream sprite (from destroyed Mideel) to new caves and new forests.
I would think it would also be possible to add new maps, since there are plenty of extra black screens (I'm thinking Mako Reactor program).