When running installation with the option to build a response file and where you have defined in autosys_secure the short hostname of the EEM server, then the installer adds the FQDN hostname also in field IA_AE_INSTANCE_EEM_SERVER_NAME .
IA_AE_INSTANCE_EEM_SERVER_NAME=hostname,hostname.example.com
Autosys 12.x and higher
It will make no difference when running a silent installation having the 2 hostnames specified in field IA_AE_INSTANCE_EEM_SERVER_NAME.