>what if, instead of accurately emulating how the GBA PWM hardware works, the emulator uses its own interpolation algorithm to resample from audio channels’ sample rates directly to the emulator’s audio output sample rate?
Then it would be less accurate to the actual console, and thus a worse emulator.
Accuracy isn't always the point of video game emulators since gaming experience is a subjective thing. Most of old games were crippled by the limitations of the hardware their run on. Inaccuracies can very much improve the experience, like removing sprite limits, displaying wider aspect ratios or in this case improving sound interpolation.
Then it would be less accurate to the actual console, and thus a worse emulator.