The reference is the same. In delta-wound configuration we have line voltages which are defined as Vab, Vbc, Vca. From the control point of view there is not much difference between wye and delta but some inputs are not directly available. Line currents must be converter to phase current and an offset is need in the electrical angle used to compute dq currents.
Check out this example where you can switch beetween wye and delta using hyperlinks:
