Direction of E1 and E2 in phasor diagram of transformer
If primary winding and secondary windings are wound in the same way then E1 and E2 will be in phase. Consider this diagram and the first three scenarios: -



Scenario 1 shows an idealized single turn primary winding with V applied. Scenario 2 considers what happens if the single turn is in fact two closely wound parallel turns.

Scenario 3 is a small jump from S2 in that it asks you to consider that if the second winding (in S2) were disconnected from the 1st winding, the voltage on its terminals would have the same phase as the primary voltage.

Justification for this comes from the fact that if you reconnected it back to the first winding there would be no sparks or fire and this is intuitively what you'd expect for a primary and secondary wound in the same way. The "same way" can only mean both being wound either clockwise or anticlockwise around the core.