Here we have the original trucks, couplers, and height of the car as it comes from Atlas.

Here is the result after setting the car down properly.

The excess height to clear hirail flanges is obvious, and how it's disguised is not very subtly done if its disguised at all. First, the factory uses the same trucks with the same bolster width and huge journals for highrail, unmodified other than to put wheels/axles in to 2-rail standard. The height off the trucks to clear the hirail wheels also remains in the 2-rail version. Yet, the factory couplers hit the gage. The boxes tell a lot of the story, very thick between coupler shank and underframe to lower the coupler, and a pad cast on that lowers it even further.
The Kadee box is much thinner up top, allowing one to line the axis of the coupler shank with the axis of the frame, thus the draughtgear is put into proper relationship with the rest of the frame.
Chuck the hi-rail (albeit factory two-rail) trucks for scale trucks, and set the truck height such that the coupler meets the height gage, and the appearance overall falls far closer in line with the height of the prototype off the trucks and in general. This car came down almost a scale foot. As a good friend commented, "Once you see it, you can't unsee it". The improvement is pretty dramatic.