I'm afraid RailClone does not have functions to manage smoothing groups, these are retained from the the source geometry. That said, it looks as though you have vertex weld switched on? If you turn this off the corners will remain sliced and you will get nice clean edges. There shouldn't be any need to weld the corners for this kind of setup.
The only other alternative is, as you mention, to add a smooth operator. Normally this would remove instancing support but if you are already using vertex weld then this also has the same effect.
I hope that helps,