3 foot of water in a car does indicate something.
Alt shorting is likely but i would expect battery light to illuminate at that point.
Location of alt does matter. A low one could in theory short earlier than a higher located one so i dont agree with the dont matter theory.
Dead alternator bearing only binding enough so when belt is wet could in theory cause issues although very unlikely.
Old belt that has lost tension could be likely.
Its an interesting problem IMHO and look forward to the answer.

