I still don't get what you mean by "choke". A series inductor? Between where and where? Or a common mode choke?
A transformer is all about currents. A current in any of the 3 windings will induce a voltage in every of the 3 windings (proportional by M_ij or L_i respectively}. This doesn't do anything per se, as long as this voltage doesn't cause a current (canceling the voltages in the other windings per Lenz's law).