Yeah but the beep had an envelope to it. There was definitely a strong attack followed by a less-than-square wave rather than a uniform beep. Though whether that was part of the sample (which the mac SE definitely could've played) or an artifact of some analogue circuitry I don't know.
Not sure what process generated that tone, but it really was a bell-like BINNNNGGGG and not a flat PC buzzer-like BEEP. At least, that's the sound I remember from the 512K and the Plus - I never had an SE myself, so I am assuming it used the same sound as the original models.