A phase shift and a time shift go hand in hand but it really does depend on your reference frame. For example, in a three-phase generator all of the voltages start at the same time so they all have the same t0. But from a different reference frame, we could consider the time that they peak. In that frame, the time of the positive peak (tpeak) will be different for the voltages. With the three-phase generator, we produce a shift by a physical shift, just like I did for the voltages on the left side of my generator example.
Using the winding voltages in different ways does not produce a real time shift for t0 in one reference frame. But if we look at the positive peak times (tpeak) for those voltages, they do occur at different times.
The other way to get a shift is to actually delay the waveform. You could do this using delay boxes. I have a delay cascade circuit that I use on my workbench to get a 3-phase set of voltages from a single-phase source. The time shift due to flux lag from the primary to secondary side of the transformer is another example of a time delay.
This actual time delay appears to be the shift you are thinking about, but is not the phase shift we normally talk about when discussing transformer phase shifts. Outside of the shift from the flux delay (which we routinely ignore), the transformers do not have that kind of time shift.