When I get RB450G's from a certain vendor, the pc speaker has a different startup beep than normal. I've read how to do this with /system scheduler and /system script, but the default configuration does not have anything set up here. How, then, did they change the startup beep?

The different beep means that the device wanted to find Flashig, but didn't, so it started with default settings. New devices should be arriving with Flashfig enabled, so that you can mass-configure them very quickly.

Read more about Flashfig:

http://wiki.mikrotik.com/wiki/Manual:Flashfig