Hi Gourav,
I think you can't update manifest file directly in OutSystems. You can update some property by making the changes in extensibility configuration. In this you need to pass value as name-value pair. Like in your case property name may be debugger and value may be false. Please refer below link for more information :
https://success.outsystems.com/Documentation/11/Delivering_Mobile_Apps/Customize_Your_Mobile_App/Set_the_Preferences_for_Your_Mobile_App
Apart from this I found one forum discussion, according to that you can create a blank plugin with all configuration in manifest of plugin and then use that plugin in your application :
https://www.outsystems.com/forums/discussion/63862/setting-android-feature-flags-in-manifest/
Regards