I think I figured out what the super secret addition is:
Save Render Targets to File? (under Dev Tools, of the launcher flags)
Nope. That's just a standard part of the envmapping support that I added. This is for modders to save the envmaps generated by the game to file. Then they can enhance/compress them and distribute the files as part of the mod/mission data. There is a new mission flag ("$Environment Map:") which lets them specify a file to use for the envmap.
When you enable that option (-save_render_target) then it will save the generated envmaps, and other static render-targets, to data/cache/ so that you can pick over them later. So when the ship/weapon select screens are modified to use the render-to-texture support to turn 3D models into icons, the mod maker can save those images and use them as the icons for the ship/weapon. And since the OpenGL extension required to make envmaps in-game isn't going to be supported for everyone, this lets them still get to use envmaps since they already exist.
As an added benefit of this, it can save a ton of memory. When an envmap is created by the game it's uncompressed. With the default settings that means that the envmap is using about 6megs of memory. But if the mission maker was kind enough to distribute an envmap which was already created, and compress it with DXT1, then it would need only 1meg of memory. Plus the saved envmap could be enhanced to highlight certain portions or some parts even removed. Hell, you could make a totally new envmap from scratch, or from images downloaded from NASA, and use that instead of relying on the game to do it for you.