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Generally speaking, you can do either way (with or without phase shift) as long as you are consistent with all the transformers. Y-Delta transformers are mainly for generator step-up and nearly all the generators are connected by Y-delta step-up transformer. When we do the dynamic simulations, we are comparing relative angles, rather than absolutely angle. So the phase shifting effects are cancelled out already.

In terms of short-circuit calculation, there should not be any difference. You may see that the phasor value of short-circuit current is different (i.e., the real and imaginary part), but the magnitude should be the same.

So, the point is that no matter which practice to be followed, it should be consistent with all the transformers. Otherwise, wrong results will be expected.