Tim, Welcome to the Forum.
Is the isolation transformer part of the manufactured equipment ?
If it is, the entire unit including the transformer may be covered by the equipment listing.
If the transformer is separate from the equipment then it most be protected in accordance with 450.3 and the conductors protected in accordance with Art 240, most likely 240.21(C), but being 480 to 480, your primary protection would most lilely be adequate as secondary protection.
Can you provide some more detail ?