Thanks for the question.
This particular usage isn't really an Arnold limitation. The box mapping feature was intended to create seamless UVW mapping along the length of the final spline, in this example, we're trying to do something a little different.
That said, I've attached a solution that appears to be working OK. To achieve it I've had to take into consideration that the UVW Modifier rotates and offsets from the start of the spline, not per object. Knowing that we can use a bit of trigonometry to try and offset and rotate the UVs to reverse their new orientation and position along the spline.
In any case, it might be easier to UV map the geometry before adding it to RailCLone for this kind of thing, alternatively, you could create the nested geometry as a separate RailClone object and then import it using a Segment node. Since you need to disable instancing anyway to use UVs, there would be no performance hit when using this technique and actually you might find it's more efficient because you could leave instancing enabled for the second RC object. I've added a second file to illustrate this approach.
I hope that helps,