I've thought about this too. I know bigger always seems to be better, but does anyone REALLY want their undercharged battery charging @ 100 amps? LOL I would think even a 50 amp alternator would be fine.
That is not how it works, the voltage regulator limits the voltage. The 100A unit has the ability to supply up 100A, but the load dictates the current. A discharged battery has a high internal resistance that limits current.