[skidlids]

The Alternator should make maximum output when New/In Good Condition, if it has a fault such as a short across some windings then its output would be lower, so I can't see how it could put out more and hence damage the Rectifier/Regulator.
Have you checked the condition of the Charging fuse (the 40A large one)and its connections to make sure the voltage output from the regulator is getting to the battery