If you want to start from scratch I would download 1.1b2 and run the Uninstaller that comes in the .dmg, which should remove all vestiges of Startup Sound.pref from your Mac.
Normally the System Volume controls the volume of the Startup Chime if it is the last thing that you adjust before you Shut Down your Mac. For example, if you set the System Volume to the level at which you want to hear the chime and then Shut Down your Mac, when you Restart your Mac, that should be the volume level that you hear the chime. Likewise, if the last thing you do is mute the System Volume and then Shut Down the Mac, when you Restart the Mac, you should not hear the Startup Chime.
The one caveat to this is if your Mac has been sleeping. If you waken your Mac and immediately Shut Down, when you Restart the Mac, the Startup Chime will be muted. To insure that your Startup Chime is not muted, after you awaken your Mac, either play a sound intentionally or adjust the System Volume, then Shut Down your Mac and when it Restarts the Startup Sound should be the level that you have set.
On my iMac Intel, even though I have external speakers, the Startup Chime plays through the internal speakers. On my old iMac G3, with external speakers connected, everything plays through the external speakers.
The Startup Chime is your Mac alerting your that it has passed the POST (Power On Self Test), and that the Test has found usable RAM installed at startup. iMacs, based on the model, have a series on Alert Codes, chimes, beeps or flashing power indicator lights, that alert you when the POST encounters problems.