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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. 

Those are good questions.

I have seen songs, Castlevania comes to mind, where they will add or subtract 1 pitch unit from one of the square channel (by setting a single value of -1 or + 1 in the using the "Pitch" effect track on the very first note of the song). This seem to break the interference that you mention and it creates very interesting effects. Channels become much more audible all of a sudden.

I didn't write the sound emutation for the base NES (i did write some of the expansions that were missing tho) but it should be fairly accurate. It will not be helpful at all for you, but "the phase of the square channels resets every time hi-byte of the 16-bit period is written". That was quite a mouthful. In plain English it means that the phase will only reset when you cross over these notes (approximately) : A-3, A-2, D-2, A-1, F-1, D-1. I dont think its realistic for you to purposely reset the phase in your songs...

I just have an Everdrive N8. The base version (need to get the pro soon) does not have an NSF player, so i use my ROM exporter. And no, i dont have any mods so if i were to use expansion audio, it would be emulated by the Everdrive... which would kind of defeat the purpose of using real hardware. I heard of people having boards with VRC6 and other expansions on them, but I dont know much about those. If you have a Famicom, getting an FDS would be super cool. That's the one expansion chip that anyone can get and run on actual hardware easily.

-Mat