With "Run CGI scripts as Domain owner"..Yes and CGI wrapper (run as virtual server) Install Joomla at the "root" of a site.. Then try to start over..
Uninstall fails can not remove the cgi-bin/php5.cgi Removes all files but not Virtualmin data..
I must chattr -i the file or move the file then do the uninstall and put it back after it is done.
It would be nice if they could start over by doing the uninstall/reinstall without issues.. I know this is with joomla.. I bet other CMS php systems could have the same problems..