OK! As I said I didn't followed the guide you posted (looks very complete), mainly I just modified:
And finally added an etc folder with the config from the "bin" path of the last version of WinAVR. I am not sure if all boards will be supported, I only have Uno and Mega to test, but hex size is now couple bytes smaller always.
Also full size is now 39 mb now! including java (too much crap in the original winavr directory)