You could create the backup script in a folder protected by a DACL and only the SYSTEM and admin can access it. That way the command line of the scheduled task will not have the password clear text. The script will though :/ But protected by DACL :)
You don't need to backup the WAP server, they configuration is stored in the ADFS database. No need to restore a WAP server, you just reinstall a brand new one if you need to "replace" one.
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