I have a website project using Visual Studio 2013, and each time I open it, it keeps adding a new entry for the website project in applicationHost.config. I use IISExpress
How to: Specify a Port for the Development Server
I just tried out the method described in the above msdn article to change the port IIS express uses (didn't try 80 though).
At that point it doesn't seem to create a new entry in applicationHost.config, and uses the new port.