I'm not the one to answer this but one thing that is obvious even to me that whdload is not about emulating software made for another machine than the host system so I don't see how a comparison can be made.
As for emulating C64 on Amiga, because they are compleyely different machines I doubt there would be an alternative to writing a full emulator. Amiga and C64 are in no way compatible to each other apart from the joystick port
But of course, in theory, one would write different emulators for seperate games and optimize them according to the needs of the games emulated. Still I can't relate it to whdload or think of any sane programmer that would want to do this.