Are your 100 volt conversions overheating with a load or without one?
If you are running your rotor at 100% duty cycle with a 12 - 15 volts input it will get very hot all by itself. Most of the Delco 10 & 12SI alternators I have ever worked on or modified had a rotor winding resistance of around 4 - 5 ohms. At a 12 - 15 volts input that equates to as much as 60 watts of heat being built up in it all by itself and unfortunately by the design of most alternators the rotor itself sees the least amount of cooling effects.
As far as physical stresses go unless you are running the 10/12 SI units at 20,000+ RPMs and the bigger ones at 15,000+ RPMs I would have serious doubts about any negative physical stress issues on the rotor itself.
Over tight belts, or over long belts dancing around, would do more harm than anything and that is still limited to the bearings unless the alternator is poorly secured by what ever mounting methods you used.