Not sure of all the termoinology, so please forgive me...
On my server, if you go to yourdomain/myadmin you do not see the content of that folder, you see the content of http://console.host2help.com/
which allowsd me to put site management tools in every domain with a small disk footprint, and makes managing updates a breeze.
However, the ajax uploader (which works beautifully on our server - nice code!) gives java errors when installed like this. I am guessing that the isssue is down to the path being discovered through php, because sometimes php reports the physical path, sometimes the virtual, and the crossover is causing headaches.