He's right, its that simple. But if you watch the Lionel video, you may understand what your doing too. Even changing an outlet can change the phase.
And near zero isn't always what you see. An AF and a Marx I have give 8 volts in phase at around a 15v setting. Out of phase its about 22v.
Fyi, Some transformers were assembled by Lionel out of phase to the cords plug's fat side. I think a brick and a CW80.
On yours the breaker tripping should be nearly instant as the breaker is electronic vs thermal.
Could you clear up how the engines in the yard are reacting in case phase isn't at fault. Something might be triggering a reset into conventional mode too, but so far the approach is old school.