If Scalar mode is required, then, yes, limit the current.
However, if the motor is dual wound for 480VAC and 240VAC, then you don't really need the transformer and you can run DTC. The motor would be connected for 240VAC but, since the insulation is good for 480VAC, it can stand the 650VDC PWM pulses without the transformer.
Simply connect the motor as a 240VAC motor, connect it directly to the drive output terminals, and enter in Group 99 a 480V motor, 120hz. As long as the motor does not go above 60hz, it will never see more than the PWM equivalent of 240V.
Is this clear or have I confused the issue?