When ordering through WHMCS for VM, the automation assigns the IP address but does not actually put the IP address on the server. Is this any issue OR a time taking process?

It seems to be an issue because Hosting Controller specifies the password, hostname and ip address properly upon VM creation. Can you please let us know which version of Hosting Controller are you using on your Server ? Also, share the details of OSTemplate being used so you may be guided appropriately about it.