Hi there, I am the creator. As other commenters pointed out, the vertical distances were exaggerated roughly 4x so things don't overlap each other.

I have experimented with a few things over the years and this is my latest series: https://www.projectsubwaynyc.com/complexes I think they look more reasonable - still legible but the stairs and escalators look more to scale. They also include elevators.

I don't know about this instance in particular, but the vertical scale in similar maps is often exaggerated to make it easier to differentiate the different floors.

At the cost of distorting elements with a vertical dimension, it means that all the wireframe layouts don't end up overlaying each other.

They are schematic drawings to make them clearer, not to scale.