Things a total conversion would want:
1) Own icon (when running)
2) Own icon displayed in the operating system.
3) Own window title
4) Own application description
5) Possibility of indicating the gamedata directory
#1, #3 and #5 could be done via cvars.
#2 and #4 cannot be done via cvars. #4 can probably be done just renaming the engine.
That leaves #2.
Supposedly with this tool you can open the .exe and literally edit the application icon for an .exe.
However, the oddity with that: although a discouraged practice, any "security module" that relies on a checksum of an .exe would break. Not that such a thing is even of any true use as far as I know on a non-Windows platform. But on Windows since process ids or what not can be tied back to the true executable, it is rather difficult to deceive a dll as I understand it (at least in this particular way).