tempfiles are only used by tablespaces used for storing temporary segments. In which case, it is locally managed.
If I understand correctly, tablespaces likes these (ie temp tablespace) don't requiry media recovery and do not require to be backed-up.
I've tested and found that if a tempfile was deleted from the OS, the instance will still startup normal. You simply need to do what it is you need to do to fix this.
I'm interested to clarify this because I have a HOT BACKUP scripts that dynamically creates the scripts that backup the tablespaces. It complains when it gets to the temp tablespace and tries to put it in backup mode.
So what I propose to do is simply not backup any tablespace that has tempfiles associated with it (dba_temp_files). Would this be anout correct? I'm assuming the only tablespaces that would ever have temp files associated with them are those that store temporary objects.