Another workaround to this is to create 2 directories for EXTRANET and INTRANET. Point the EXTRANET default doc to EXTRANET folder and do the same for INTRANET to it's INTRANET directory and fefault doc. Leave all virtual directories and file as is.
Each web site now will have its own default document, which I am assuming that the default document redirects to the proper virtual directory? This way you now have different IPs on the websites and directing to their own deefault document