Thanks for the question. I'm afraid at the moment there is no way for RailClone to automatically cap the open holes. The only way to do this is to apply a Cap Holes modifier to the object, but unfortunately this will disable instancing.
Another option might be to use render time-booleans. You can read a little more about this here: https://forum.itoosoft.com/railclone-pro-
I hope that helps, please let me know if you have further questions.