This tool (App -> Tools -> Batch Update Layouts) is very handy, but still is not sufficient for centralized layouts management. It would be sufficient if:
I consider the following (quite common) use case:
The app has to have consistent layouts usage, e.g. we need to have all "regular" pages (opened in Content = non-popup layouts) to use the same layout.
It would be nice to have this tool even for pages developed in our app-specific modules, but especially for Marketplace modules that are used in the app (e.g. Setting for MxModelReflection, [User] Administration, Excel Exporter and Importer, Email Connector): we want to set all of them to "our" layout after importing them and after each re-importing for version upgrade.