there is nothing that prevents you from getting rid of the tsconfig.app.json. it’s just an additional config file that allows you to adjust your configuration on an app basis. this is e.g. useful when you have multiple apps in the same angular-cli workspace.
you could have the root folder with the tsconfig.json and then a sub folder app-a with a tsconfig.app.json file and another app in the sub-folder app-b with it’s own tsconfig.app.json, which contains a variation of the global configuration.
the difference in configuration could e.g. be the output directory outDir or the includes or excludes used.