An isolation transformer is a separately derived system and must be grounded per article 250. It makes no difference if there is a grounded conductor on both the transformer primary and secondary, you must follow correct grounding and bonding practices.
But wouldn't having an isolating transformer with both of the windings grounded be a waste of time, considering that the ground connection would be common to both windings?.
I was always under the impression that a double wound transformer was made so that there would be no reference to the primary winding by the secondary winding, hence the term isolating transformer.
