Hey Nahid,
Apologies for the delayed response.
Sure, so our use case is that we use WPEngine to deploy our site. So we have both a Staging and a production WordPress instance. When we deploy Staging to live the DB is copied too so if the Staging instance has a Netlify hook for a Staging deployment then live would inherit that Staging hook rather than persisting a production hook.
I think other plugins get around this by allowing you to set a config option in the wp-config.php file. If set, your Netlify plugin would use that value as the hook. Otherwise it would use the value defined in the UI.
I hope that helps. Happy to provide any more info if needed.
All the best,
Eddy