On a rooted device, either data can be stolen or application can be changed,
The SecureChannel specific payload is submitted to serve as part existing payload. On the server side the first call is made to the SecureChannel API. If the API does not receive the required data then it rejects the request.
SecureChannel just produces a json package which should be passed to serve as part of your existing payload. It is up to the application how it passes payload to the server. Thus, it is application type independent.
SecureChannel web based cockpit provides extensive identity and access management of users. But, in most cases, explicit management is not required, as the system automatically takes care of most of these activities.