Adding more channels does nothing to the overtone information. From what I can find[1], it seems that the phase of the 25% and 75% waves are such that the two waves are actually inverse of each other. I don't know much about Gameboy hardware though. Do you actually know what the point of this is?
Sure, but having a channel with 25% duty cycle of frequency f and a channel with 75% duty cycle of frequency 3f will lead to a different waveform after mixing compared to 75% at f and 25% at 3f, no?
Depending on how that's processed downstream it could sound very different I imagine.
In crude ASCII art (two inputs mixed to an output):
[1]: https://gbdev.gg8.se/wiki/articles/Gameboy_sound_hardware#Sq...