Instead of including config.json, web.config and appsettings.json files that break my instance after installing an update include them with a default_ or example_ prefix.
That way I can just take the folder with the new Universal files and have someone paste them over the old ones. Now I constantly need to assist the IT staff because we don’t have access to the application servers.
You should only need to touch settings files at the original point of installation and when something changes in said settings.