I found a page for the Linux sound drivers for PowerMac which mentioned similar issues with the sound volume with the Toonie chip (Mac mini G4) which may be solved with a new driver "snd-aoa": https://wiki.debian.org/PowerPC/SoundCards.
In another thread, someone pointed to the fact that the patched ROM makes Mac OS 9 treating the Mac Mini G4 as a Cube which had no built-in amplifier for the sound volume because it was meant to run with special speakers (Apple Pro USB Speakers) which had itself the amplifier for sound: http://macos9lives.com/smforum/index.php/topic,2408.msg52465.html#msg52465.
In another thread, someone pointed to the fact that the patched ROM makes Mac OS 9 treating the Mac Mini G4 as a Cube which had no built-in amplifier for the sound volume because it was meant to run with special speakers (Apple Pro USB Speakers) which had itself the amplifier for sound: http://macos9lives.com/smforum/index.php/topic,2408.msg52465.html#msg52465.