not gonna edit it because i don't wanna interfere with your overhauls, but just for the sake of mentioning:
2A03 duty setting 1 and 3 are not identical, 3 has an inverted phase compared to 1, which sounds the same by itself but behaves differently in a mix.
if you combine the two together you can notice it sounds very different than just stacking two duty 1 pulses together - it's a trick that i don't actually see used all that often in tunes, probably because it requires sacrificing both pulse channels to achieve which is a bit of a luxury
looking forward to the overhauls!!