>>BR0282E Directory 'E:\oracle\CND\security\rsecssfs\data' not found<<
The SAP note 1764043 - Support for secure storage in BR*Tools is the answer to your issue.
You need to manually create the directories $SAPDATA_HOME/security/rsecssfs/data and $SAPDATA_HOME/security/rsecssfs/key as suggested in the note.
After that you need to create the brt$adm user at the Oracle level and change the password.
BR*Tools is not pointing to the incorrect directory. The one under SAPDATA_HOME is the one used by BR*Tools.