OK so i edited the original virtual hosts and just changed the doc root from /var/www/html (or htmlssl for my custom one) to /opt/kaltura/app/alpha/web and i can still access my webmin using the special port so thats good.
So the answer to the original question of the topic is NO... 
Now i am no longer getting the fail on
API cannot connect to https://hostname.example.com/api_v3/index.php?service=system&action=ping