As long as you have effects to separate chorusing channels into single channels (say, Pxx), things will not sound harsh unless there are too many channels chorusing at once. However, it is true that 2A03 50% square waves are very likely to sound harsh when the volume is high.
I've tried chorusing & learned the hard way when nicetas_c was helping me out with my last track; it's not a good idea to do a chorus if all your square channels have the same duty cycle (the notes will end up either killing each other or building on top of each other). So, besides adding different effects like a pitch bend or a vibrato, make sure that you used different duty cycles for different channels as well.
I find the best way to chorus with the same duty cycle is to make the pitched/vibrato (really anyone's preference) track of a lower volume than the non-pitched/non-vibrato track, if that makes any sense what I just said. That's just me, though.
Sorry for the deviation, but I just couldn't help chiming in.
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Indeed, that makes a lot of sense. With a difference in volume between channels (& the fact that one channel's using a pitch-bending effect,) the sound waves will be modified just enough to prevent the waves from building on or destroying each other.
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