Thanks for reporting this. This occurs because the Limit to material ID function is expecting the array to use a spline for the X Axis. When using a clipping path RailClone is essentially using the X and Y size parameters to set the array and then clipping afterward, so it's working in a different mode. There are a few difficulties such as what would happen if a spline contained segments with different material IDs? I'll report this to our development team and see if it's possible to add this feature.
I can confirm that it's not possible to drag a node out from the Clipping input in an A2S array, I've reported that as a bug.
Many thanks for the feedback,