Is there any known method you are already using to fetch FQDN on those machines? For example some command line tool, shell command, etc.? Does output of any of following command:
scutil --get ComputerName
scutil --get HostName
scutil --get LocalHostName
mention value that could be possibly used as FQDN?
We have already seen machines that were configured in a way that they were not aware of their's FQDN, it was available only on DNS servers, but that is problem for ESMC Agent which requires data to be available locally.