Sorry to resurrect an old thread, but this is still a problem in 2013 with NPM V10.5. The Configuration Wizard cannot handle HTTPS, FQDN, and SSL settings. If you tell it to use port 443, it creates a new primary Website ID in dbo.Websites with just the hostname, port 443, and SSLenabled set to 0. You can edit this in SQL Studio. I delete the new entry, and change the old one to primary.
The Wizard could and should examine the existing Website entry, and propose it as the default. Many sites are forbidden to use HTTP.