It is very awkward and I never understood why YOURLS does this. Last time I installed it I ended up using “Site Publisher” tool in cpanel to publish a basic landing page at the URL to hide them (it shouldn’t conflict with your install there).
I have a little 4 file template I use for sites where I do not want to expose the file directory via a URL. e.g. http://lab.cogdogblog.com it uses jquery backstretch to fill the background with an image of your choice.
Just wrote up an activity to show you how to do the same thing