I'm afraid at the moment is isn't possible to automatically generate junctions using RailClone. This feature has been on the wishlist for a long time, but unfortunately it involves several technical challenges, futhermore RailClone is designed to be a generic tool, so we cannot assume certain shortcuts that would be used in a specialized road making tool. Genuinely we would like to dedicate some time to this problem, but at this point there are too many features in the to-do list, and not all of them can be implemented. We'll continue to look into it.
In the mean time you might find a response from Klonsemann in this thread is helpful: http://forum.itoosoft.com/index.php?topic=3418.msg13419#msg13419
He solves the issue by adding half a road to boundary splines and filling in the gap in the middle.
I hope that helps, please let me know if you have any further questions.