Answer
Yes, GFI EndPointSecurity agents can be deployed to a domain that is not the same as the one where the GFI EndPointSecurity server is located, as long as the computers in that domain are visible from the GFI EndPointSecurity server.The NETBIOS name or IP Address can be used to refer to computers in the other domain.
Please review the following article for additional requirements to deploy the agent: What is required to install the EndPointSecurity Agent on a client machine?