Websites on Wiki server
I don't think you can on the same hostname as the wiki server. I ended up setting up new subdomains and hosting stuff there. Just create a new site in the Websites service and drop your files in there.
If you look at the default index pages on the default sites created (non-SSL and SSL) you'll see it loads index.php, /wiki/, /xcode/ and sometimes some other stuff. You can remove the /wiki and host sites on the primary domain but I think that breaks wiki access.
Subdomain it. And then create your DNS CNAMES/aliases on your server and domain registrar.