The manual implies that you can decouple the flash and exposure compensation in the custom menus e-4. Not quite sure what this means in practice. I hope that with this set you can adjust only the flash setting or only the exposure setting.
I don't know if this feature has been mentioned before but it was first introduced in the D4 and D600 and now apparently in the D7100. It is not available in the D800.
Normally when you have the camera in 3D matrix metering mode and iTTL flash you will be using CPU lenses which also furnish distance information. The camera will take into account this distance information and meter for the background to give a more balanced exposure to the overall scene. In the camera bodies prior to the D4 and D600 exposure compensation will be applied to the whole scene and if flash compensation and metering compensation are both used they will add.
With the new split exposure compensation it appears you will have more control over the background separate from the flash target. I don't think it will work in spot metering mode as iTTL mode is disabled.
Anyway I think this is the way it will work but I don't have any of the new bodies to test it out. Maybe someone with one of these bodies can try it out or explain it better if I'm wrong.
I use this with the D4 and I can tell you it is terrific. With the D800 and older designs, if your lighting is set and you want to drop the ambient light, you lower your exposure compensation and then raise you flash compensation to get back to where you were. With the new option, you can adjust one without affecting the other. Just simpler to keep straight in my mind. By the way, it is an option. If you are combining use of a D800 and D7100 (D600, D4) you can leave it set to the default and your cameras will operate identically. I think this is a great feature.