210.9 says "Branch circuits shall not be derived from autotransformers unless the circuit supplied has a grounded conductor that is electrically connected to a grounded conductor of the system supplying the autotransformer." 215.11 is similar.
So I don't think that actually says that the grounded conductor has to be connected to the autotransformer, just that the circuit supplied must be connected to the grounded conductor.
You agree that only 2 out of 3 of the 240/480V system conductors can be connected to the autotransformer, because of the circulating current issue?
Cheers, Wayne