I assume MojoPortal makes changes in applicationHost.config file
No, possibly Web Platform Installer does but not mojoPortal. mojoPortal is just a web app that runs in IIS it doesn't control or configure IIS.
"http://www.serverDNS.com" points to the mojoportal subdirectory
no dns names point to ip addresses not folders so I don't know what you mean by that
the "basic settings" of the "Default Website" shows the physical path to be "C:\inetpub\wwwroot" - yet, the de facto physical path is "c:\websites\mojopotal"
I have no idea what you mean by de-facto, an IIS web site points to whatever folder it says in Basic Settings there is nothing that changes that.
I suspect the actual problem is that you created (via platform installer) another IIS web site that is conflicting with the default web site. So in effect there are 2 default web sites and that causes both of them to break. The second web site needs a host name on its bindings to differentiate it from the default web site. The thing that makes the default web site default is that it has no host names, there can be only one IIS web site for a given ip address that has no host names in the bindings. As soon as a second site is configured that way it breaks one or both sites.
So if a new IIS site was created for mojoPortal by platform installer and it broke the default web site you either need to add a host name to the bindings of the new site or delete it completely to repair the default web site.
Hope that helps,