I could probably make some kind of interference test demo. Playing octaves or unisson typically results in some unpleasantness. Using different duty cycles helps but the best cure I found is to use a tiny amount of vibrato just to force the waveforms out of phase. But it is not 100% and once in a while a note kinds of craps out.
I am quite curious about the inner working of the sound generator in this regard. The annoying part is that the waveforms are seemingly never aligned exactly the same each time you play the same song, which makes fixing the occasional phase interference weirdness difficult. Is emulation accurate to the real hardware in this regard ? If so, are there some techniques to better control this aspect when you make music ?
Btw is your NES modified to play expansion audio ? I have a Famicom and I am contemplating getting a flashcart for it.