I use settings with unchecked option 'Show default folder/file icons from Explorer' and have no 'IconLib=' setting in wincmd.ini so TC overlays icons with this symbol.
I've read these topics:
http://www.ghisler.ch/board/viewtopic.php?t=45252
http://www.ghisler.ch/board/viewtopic.php?t=45358
http://www.ghisler.ch/board/viewtopic.php?t=45523
http://www.ghisler.ch/board/viewtopic.php?t=46634
to figure out how exactly icons are rendered and what problems with it remain unsolved.
I support the suggestion from Zerryk:
change the default icon for junction to something like this, at least when overlays have to be shown:
Image: http://jpeg.cz/images/2016/11/27/lDwaK.png