The new layout wasn't design as a plan, but as an illustration. As I previously said, I was rather interested in composing and framing a scene to create a plausible small universe.
In that respect, I first draw an elevation of what I wanted, composing the scene as I've witnessed in Japanese gardens last month. First, the elevator was set on a corner then forested areas were created in front of it to frame the action as railcars are pulling in front of the building. The idea was to have the impression the person looking at the layout is standing in an open field or clearing and can only grasp a part of the train.
Second, I thought it would be better to compose the scene as a succession of planes rather than create hard to conceal things like perpendicular road. It means almost everything is parallel to the tracks, which emphasized the linear nature of a railway. In fact, this is not to different from the way traditional animators created scenes by using several planes to build up the illusion.
Finally, as you can see, the foreground forested areas are carefully located so they not only frame the view but aren't a hindrance for operation. The turnout may not be visible, but it's not important since no uncoupling occurs there. Also, from experience, I know we rarely observe a train while standing by a stand switch.