GoAnywhere Director has an encryption tool that is accessible via the Tools Drop-Down menu. You can enter any value you want and it will generate an encrypted value for you based on GAD passcodes. You can always copy this encrypted value into your system and send it to the Project and utilize it as an encrypted value as long as you identify the Parameter as an encrypted value in your project.
Otherwise, there really is no way to generate an encrypted value "on the fly" from the iSeries RunProject command to pass the encrypted value.
One option might be to have a GoAnywhere Project encrypt values and place them into a Data Area then retrieve the value from the Data area before making the call.