Thanks for your suggestions on this. Your setup is a little different, but it finally gave me clues as to what functions were being called to list the directories. As a result, I believe I've resolved my issue.
In lib/moodlelib.php, the function get_directory_list checks for "(filetype($fullfile) == 'dir')" (around line 4888). I tweaked to check for "... or ... == 'link')" also, as our symbolic links to directories in every course were not being displayed when attempting to "Display a Directory". This way, they are displayed like any other standard directory.