I am not yet using the Autoloader mechanism personally (looking into doing so; this thread is helping me to better understand limitations), but currently using Registry to do so at startup, and at least there (in the registry) the ..\Applications\ key is processed alphabetically, and loaded in kind (i.e., "_App1" loads before "App1", etc.)... Perhaps the same works with bundles?
Regardless, you'd still need to check for write-access prior to performing the update in the event another process (offline files, etc.), or session has locked the file(s) / folder(s).