Well that would be a problem all right, but we were talking about momentary mains voltage droop do to an air conditioner turning on. Mains voltage droop is unlikely to cause the 5 volt regulator to short out (the problem you had - outputting 12 volts).
Well designed supplies take into account the price of the motherboards they power. There should be an OVP (over-voltage protection) circuit on the logic supply.
Many/most computer supplies only regulate the logic to a precise value and depend on the others to stay in regulation solely by virtue of the transformer turns ratios - the 12 V supply can't go over voltage because there is no excess voltage there. The logic supply has active components to regulate the output.
The OVP circuit triggers a thyristor (SCR) into conduction clamping the 5 volts to zero (actually below a volt), if the regulator is shorted the OVP may cause the fuse to blow, protecting the motherboard.
If the OVP is triggered by a transient that puts a high voltage spike on the logic supply, the inherent current limiting protection protects the regulator and shuts down the drive to the oscillator. That's what was happening when I'd turn the speaker wall wart "off" on my system - the 5 V supply would crowbar because of the transient on the 120 mains and take all the supplies down with it - resetting the computer but protecting the motherboard. To reset it I had to turn off the power mains for a few seconds then power back up. Reset switch has no effect in that case.
To cure it I put a 100 ohm resistor in series with a .05 microfarad cap across the switch. That absorbs the power that would normally create an arc that causes the HV transient. A ferrite bead on the supply line was redundant but should keep any fast rise time transients off the line.
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