What is the difference between repository database backup (using e.g Oracle backup command) and a backup made using Informatica Administrator (Actions --> Repository Contents --> Backup)?
Backup taken using Informatica Admistrator can be used to restore the repository contents in any other database type (eg. Sql server). The tool will take care of the metadata contents according to the target database server/Informatica domain.
Oracle backup command will keep the data intact and you may hit problems when you try to restore and add the repository in another domain.
There are less chances of metadata corruption if you use the Informatica Administrator to backup/restore the metadata.