A backup file contains only the library that was active when it was generated. I do have the fix coming that you asked for where it won't change the active library in the settings, but that has nothing to do with which library was included in the backup and also you can just uncheck the option to restore settings to get around that issue until the update comes out. The only thing you've said that I agree with is that the synchronize option lets people keep their own annotations if that is required.
Mike
Mike