fqdn: if there are servers w/ the same name and different fqdns, you know which one you are talking to.
Yes we have this scenario like servers having similar name but having different fqdn. In some cases we can able to communicate through TSSA for both the entries But in some cases any one is functioning properly. Just to avoid duplicate server entries in TSSA we planned to add servers with non-fqdn but I am not sure if it is best practice or not.
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you have two different servers w/ the same shortname right? server1.example.com and server1.example.net - those are two different servers. if you register 'server1', then that's going to resolve to whatever tssa appserver resolves via its dns search path. and then you will be managing only one server, not two. if you want to manage both of those servers, you need to register both of them. and i'd say even if you only want to manage one, you should still register it w/ the fqdn so you are sure which server you are managing.