Robbie D,
If you read 28-104 carefully it states the wire ampacity (Supply conductors to a motor connection box) is to be based on 75deg C conductor insulation except for Class A rated motors.
Its really not much of an issue though, if you check out table 2 based on the 2 scenarios you posted above, conductor size for either 75deg or 90 deg are the same. There is no difference in the two columns until you get to #3 or larger conductors
