About the only fix Linux could make is to ensure all audio channels are
muted as the system goes into shutdown, reboot, sleep or suspend.  That
still won't stop a directly connected beeper though.

You're making it sound as if I wanted to prevent firmware-caused beeps. I don't. I'm pretty sure that the beep I'm complaining about is OS-caused, and most likely systemd-caused. The links to other people's complaints confirm my experience.