I'm a bit confused. If you use --without-sdl-audio, there should be no difference with respect to audio between Generator and the patched Generator. If alsa does not work, try dsp or dma or any other audio options which are available for you.
If Gens has the same problem - and I don't think they share any code - I wonder whether there isn't something wrong with your audio driver or SDL.
The ~/.genrc file has nothing to do with installing. It's created as soon as you save the options in the GUI.